Investigation of the Stereochemical-Dependent DNA and RNA Binding of Arginine-Based Nucleopeptides

Nucleopeptides represent an intriguing class of nucleic acid analogues, in which nucleobases are placed in a peptide structure. The incorporation of D- and/or L-amino acids in nucleopeptide molecules allows the investigation of the role of backbone stereochemistry in determining the formation of DNA and RNA hybrids. Circular Dichroism (CD) spectroscopic studies indicated the nucleopeptide as having fully l-backbone configuration-formed stable hybrid complexes with RNA molecules. Molecular Dynamics (MD) simulations suggested a potential structure of the complex resulting from the interaction between the l-nucleopeptide and RNA strand. From this study, both the backbone (ionics and H-bonds) and nucleobases (pairing and pi-stacking) of the chiral nucleopeptide appeared to be involved in the hybrid complex formation, highlighting the key role of the backbone stereochemistry in the formation of the nucleopeptide/RNA complexes.This research was supported by Scientific Independence of Young Researchers (SIR) 2014 (RBSI142AMA) and University of Campania Luigi Vanvitelli (Valere) to S.D.M

FK228 Analogues Induce Fetal Hemoglobin in Human Erythroid Progenitors

Fetal hemoglobin (HbF) improves the clinical severity of sickle cell disease (SCD), therefore, research to identify HbF-inducing agents for treatment purposes is desirable. The focus of our study is to investigate the ability of FK228 analogues to induce HbF using a novel KU812 dual-luciferase reporter system. Molecular modeling studies showed that the structure of twenty FK228 analogues with isosteric substitutions did not disturb the global structure of the molecule. Using the dual-luciferase system, a subgroup of FK228 analogues was shown to be inducers of HbF at nanomolar concentrations. To determine the physiological relevance of these compounds, studies in primary erythroid progenitors confirmed that JMA26 and JMA33 activated HbF synthesis at levels comparable to FK228 with low cellular toxicity. These data support our lead compounds as potential therapeutic agents for further development in the treatment of SCD

Anterior gradient protein 2 promotes survival, migration and invasion of papillary thyroid carcinoma cells

Through a transcriptome microarray analysis, we have isolated Anterior gradient protein 2 (AGR2) as a gene up-regulated in papillary thyroid carcinoma (PTC). AGR2 is a disulfide isomerase over-expressed in several human carcinomas and recently linked to endoplasmic reticulum (ER) stress. Here, we analyzed the expression of AGR2 in PTC and its functional role

Benzodeazaoxaflavins as Sirtuin Inhibitors with Antiproliferative Properties in Cancer Stem Cells

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Targeting CXCR4 reverts the suppressive activity of T-regulatory cells in renal cancer

With the intent to identify biomarkers in renal cell carcinoma (RCC) the functional status of T-regulatory cells (Tregs) was investigated in primary RCC. Tregs were isolated from tumoral-(TT), peritumoral tissue-(PT) and peripheral blood-(PB) of 42 primary RCC patients and function evaluated through effector T cells (Teff) proliferation, cytokines release and demethylation of Treg Specific Region (TSDR). The highest value of Tregs was detected in TT with the uppermost amount of effector-Tregs-(CD4+CD25hiFOXP3hiCD45RA-). PB-RCC Tregs efficiently suppress Teff proliferation compared to healthy donor (HD)-Tregs and, at the intrapatient evaluation, TT-derived Tregs were the most suppressive. Higher demethylation TSDR was detected in TT- and PB-RCC Tregs vs HD-Tregs (P <0,001). CXCR4 is highly expressed on Tregs, thus we wished to modulate Tregs function through CXCR4 inhibition. CXCR4 antagonism, elicited by a new peptidic antagonist, Peptide-R29, efficiently reversed Tregs suppression of Teff proliferation. Thus Tregs functional evaluation precisely reflects Tregs status and may be a reliable biomarker of tumoral immune response. In addition, treatment with CXCR4 antagonist, impairing Tregs function, could improve the anticancer immune response, in combination with conventional therapy and/or immunotherapy such as checkpoints inhibitors

Tailoring the Structure of Cell Penetrating DNA and RNA Binding Nucleopeptides

Synthetic nucleic acid interactors represent an exciting research field due to their biotechnological and potential therapeutic applications. The translation of these molecules into drugs is a long and difficult process that justifies the continuous research of new chemotypes endowed with favorable binding, pharmacokinetic and pharmacodynamic properties. In this scenario, we describe the synthesis of two sets of homo-thymine nucleopeptides, in which nucleobases are inserted in a peptide structure, to investigate the role of the underivatized amino acid residue and the distance of the nucleobase from the peptide backbone on the nucleic acid recognition process. It is worth noting that the CD spectroscopy investigation showed that two of the reported nucleopeptides, consisting of alternation of thymine functionalized L-Orn and L-Dab and L-Arg as underivatized amino acids, were able to efficiently bind DNA and RNA targets and cross both cell and nuclear membranes

Yeast dynamics during spontaneous wine fermentation of the Catalanesca grape

Although the use of starter cultures in winemaking has improved the reproducibility and predictability of wine quality, the main drawback to this practice is the lack of the typical traits of wines produced by spontaneous fermentation. In this study, we identified for the first time the yeast population occurring during spontaneous fermentation of the Catalanesca white grape, a variety from Campania (Italy). Yeasts were identified using molecular tools: PCR-DGGE and partial sequence analysis of the 265 rRNA gene from isolates. Eighteen different species belonging to 11 different genera were identified. Hanseniaspora spp., Issatchenkia spp. and Candida spp. were the dominant yeasts during the early stages of fermentation, while the middle and end phases were dominated by Saccharomyces cerevisiae. Four species of Issatchenkia spp., rarely isolated from wine fermentation, were found in this study accounting for the 33.5% of the total isolates. The RAPD-PCR screening of the isolates followed by partial rRNA gene sequencing proved to be a very effective approach to first differentiate the isolates and then identify yeast species involved in a wine making procedure. The results show very high yeast diversity in this natural wine fermentation and also highlight the possibility of considering interesting autochthonous strains for starter selection

Antioxidant peptides from "Mozzarella di Bufala Campana DOP" after simulated gastrointestinal digestion: In vitro intestinal protection, bioavailability, and anti-haemolytic capacity

The bioactive properties of milk and milk-products are largely attributed to the peptides released during gastrointestinal digestion. Nevertheless, no similar studies on "Mozzarella di Bufala Campana DOP" (MBC), the European name given to a unique protected origin designation buffalo milk product, are available so far. A novel antioxidant peptide (MBCP) after MBC gastrointestinal digestion was identified and its in vitro intestinal protection, bioavailability, and anti-haemolytic capacity were assayed. A 0.2 mg/mL MBCP incubation dose made H2O2-stressed CaCo2 cell line proliferation increase by about 100%. Less than 10% hydrolysis in the apical solution and about 10% concentration in the basolateral solution indicated for MBCP good stability and bioavailability, respectively. A 0.2 mg/mL MBCP incubation dose reduced H2O2-induced human erythrocyte haemolysis by 91.25%. Our data indicated MBC as a potential functional food and MBCP as a novel food ingredient, food additive and pharmaceutical, relevant in health promotion and disease prevention

Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach

: The present contribution introduces a novel computational protocol called PyRMD2Dock, which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular docking software AutoDock-GPU (AD4-GPU) to enhance the throughput of virtual screening campaigns for drug discovery. By implementing PyRMD2Dock, we demonstrate that it is possible to rapidly screen massive chemical databases and identify those with the highest predicted binding affinity to a target protein. Our benchmarking and screening experiments illustrate the predictive power and speed of PyRMD2Dock and highlight its potential to accelerate the discovery of novel drug candidates. Overall, this study showcases the value of combining AI-powered LBVS tools with docking software to enable effective and high-throughput virtual screening of ultralarge molecular databases in drug discovery. PyRMD and the PyRMD2Dock protocol are freely available on GitHub (https://github.com/cosconatilab/PyRMD) as an open-source tool