CNR Institute of Biostructure and Bioimaging

Catania, Italy

CNR Institute of Biostructure and Bioimaging

Catania, Italy
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Avitabile C.,Diagnostica e Farmaceutica Molecolari Scarl | D'Andrea L.D.,CNR Institute of Biostructure and Bioimaging | Romanelli A.,University of Naples Federico II
Scientific Reports | Year: 2014

Studying how antimicrobial peptides interact with bacterial cells is pivotal to understand their mechanism of action. In this paper we explored the use of Circular Dichroism to detect the secondary structure of two antimicrobial peptides, magainin 2 and cecropin A, with E. coli bacterial cells. The results of our studies allow us to gain two important information in the context of antimicrobial peptides- bacterial cells interactions: peptides fold mainly due to interaction with LPS, which is the main component of the Gram negative bacteria outer membrane and the time required for the folding on the bacterial cells depends on the peptide analyzed.


De Simone G.,CNR Institute of Biostructure and Bioimaging | Alterio V.,CNR Institute of Biostructure and Bioimaging | Supuran C.T.,University of Florence
Expert Opinion on Drug Discovery | Year: 2013

Introduction: Carbonic anhydrases (CAs, EC 4.2.1.1) exist as five genetically distinct families (α, β, γ, δ and ζ) in organisms all over the phylogenetic tree. Due to the ubiquity of such enzymes, the selective inhibition and polypharmacology of inhibitors is an important aspect of all drug design campaigns. There are several classes of CA inhibitors (CAIs): i) metal ion binders (sulfonamides and their isosteres [sulfamates/sulfamides], dithiocarbamates, mercaptans and hydroxamates); ii) compounds anchoring to the zinc-coordinated water molecule/hydroxide ion (phenols, carboxylates, polyamines, esters and sulfocoumarins) and iii) coumarins and related compounds which apparently bind even further away from the metal ion. Areas covered: The authors rationalize the drug design strategies of inhibitors belonging to the first two classes, based on recent X-ray crystallographic data. More precisely, this is achieved by analyzing how the hydrophobic and hydrophilic halves of the enzyme active site interact with inhibitors. This task has been eased by the recent report of β-CA-like enzymes possessing carbon disulfide and carbonyl sulfide hydrolase activities, respectively, allowing the authors to propose a general approach of structure-based drug design of CAIs. Expert opinion: Although amazing progress has been made in the structure-based drug design of CAIs, this field is still in progress, with many constantly emerging new findings. Indeed, several new such enzymes were discovered and characterized recently and novel chemotypes were explored for finding compounds with a better inhibition profile. It is anticipated that this will continue to be one of the main frontiers in the search of pharmacologically relevant enzyme inhibitors. © 2013 Informa UK, Ltd.


Monti S.M.,CNR Institute of Biostructure and Bioimaging | Supuran C.T.,University of Florence | De Simone G.,CNR Institute of Biostructure and Bioimaging
Expert Opinion on Therapeutic Patents | Year: 2013

Introduction: Human carbonic anhydrases (EC 4.2.1.1) IX (hCA IX) and XII (hCA XII) are two tumor-associated proteins, being overexpressed in many tumors and involved in critical processes associated with cancer progression and response to therapy. Both are multi-domain proteins consisting of an extracellular catalytic domain (CA), a transmembrane portion (TM) and an intracytoplasmic (IC) segment. These domains have peculiar biochemical and physiological features. CA IX contains an additional proteoglycan-like (PG) domain at the N-terminus which constitutes a unique feature of this enzyme within the CA family. Areas covered: Starting from a brief description of the main molecular and catalytic features of both enzymes, their role in tumor physiology and their three-dimensional structure, this review describes the main classes of small molecule inhibitors, investigated between 2008 and 2013, able to inhibit these enzymes for both diagnostic and therapeutic applications. Expert opinion: A consistent number of patents on molecules able to inhibit the catalytic activity of CA IX and CA XII have been recently reported. Most patents deal with classical sulfonamide derivatives, demonstrating that introducing suitable substituents on the inhibitor scaffold, good selectivity can be obtained. However, the most impressive results are related to compounds containing novel chemotypes, such as coumarins and thiocumarins. Thus, it is expected that research in next future will be more dedicated to the development of molecules containing new chemotypes and a large number of studies in such field have already been published demonstrating the role of these enzymes in carcinogenesis and metastases formation. © 2013 Informa UK, Ltd.


Alterio V.,CNR Institute of Biostructure and Bioimaging | Di Fiore A.,CNR Institute of Biostructure and Bioimaging | D'Ambrosio K.,CNR Institute of Biostructure and Bioimaging | Supuran C.T.,University of Florence | De Simone G.,CNR Institute of Biostructure and Bioimaging
Chemical Reviews | Year: 2012

A description of the structural studies on α-Carbonic anhydrases (α-CA) is presented. Main structural features of the catalytically active α-CA isozymes are described and the current state of the art on complexes of hCA II with the principal classes of inhibitors is summarized. Studies have demonstrated that cyanamide acts as a weak inhibitor of the esterase activity of hCA II, interacting with the zinc ion within the enzyme active site. Crystallographic studies have shown that inorganic anions can bind within the CA II active site, either coordinating the catalytic Zn2+ ion or not coordinating it, but being located in its close proximity in a nonmetal site. The effect of the presence of a positive, negative or neutral substituent on benzenesulfonamide CAIs has been investigated to understand the effect of different charges in the CA I and CA II active sites, to discriminate the binding to these two isoforms.


Musumeci D.,University of Naples Federico II | Roviello G.N.,CNR Institute of Biostructure and Bioimaging | Montesarchio D.,University of Naples Federico II
Pharmacology and Therapeutics | Year: 2014

HMGB1 (High-Mobility Group Box-1) is a nuclear protein that acts as an architectural chromatin-binding factor involved in the maintenance of nucleosome structure and regulation of gene transcription. It can be released into the extracellular milieu from immune and non-immune cells in response to various stimuli. Extracellular HMGB1 contributes to the pathogenesis of numerous chronic inflammatory and autoimmune diseases, including sepsis, rheumatoid arthritis, atherosclerosis, chronic kidney disease, systemic lupus erythematosus (SLE), as well as cancer pathogenesis. Interaction of released HMGB1 with the cell-surface receptor for advanced glycation end products (RAGE) is one of the main signaling pathways triggering these diseases. It has been also demonstrated that the inhibition of the HMGB1-RAGE interaction represents a promising approach for the modulation of the inflammatory and tumor-facilitating activity of HMGB1. In this review we describe various approaches recently proposed in the literature to inhibit HMGB1 and the related inflammatory processes, especially focusing on the block of RAGE-HMGB1 signaling. Several strategies are based on molecules which mainly interact with RAGE as competitive antagonists of HMGB1. As an alternative, encouraging results have been obtained with HMGB1-targeting, leading to the identification of compounds that directly bind to HMGB1, ranging from small natural or synthetic molecules, such as glycyrrhizin and gabexate mesilate, to HMGB1-specific antibodies, peptides, proteins as well as bent DNA-based duplexes. Future perspectives are discussed in the light of the overall body of knowledge acquired by a large number of research groups operating in different but related fields. © 2013 Elsevier Inc. All rights reserved.


Improta R.,CNR Institute of Biostructure and Bioimaging | Barone V.,Normal School of Pisa
Angewandte Chemie - International Edition | Year: 2011

The excited states of (dA) 4 oligonucleotides (A=adenine), including the phosphoribose backbone, were studied in water at a fully quantum mechanical level, providing an atomistic description of the main decay paths and a comprehensive interpretation of the experimental data (see picture). After absorption to exciton states delocalized over multiple A bases, the behavior of the excited state is ruled by the interplay of a number of species responsible for different spectral features. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Improta R.,CNR Institute of Biostructure and Bioimaging | Barone V.,Normal School of Pisa
Topics in Current Chemistry | Year: 2015

We review the most significant results obtained in the study of isolated nucleobases in solution by quantum mechanical methods, trying to highlight also the most relevant open issues. We concisely discuss some methodological issues relevant to the study of molecular electronic excited molecular states in condensed phases, focussing on the methods most commonly applied to the study of nucleobases, i.e. continuum models as the Polarizable Continuum Model and explicit solvation models. We analyse how the solvent changes the relative energy of the lowest energy excited states in the Franck–Condon region, their minima and the Conical Intersections among the different states, interpreting the experimental optical spectra, both steady state and time-resolved. Several methods are available for accurately including solvent effects in the Franck–Condon region, and for most of the nucleobases the solvent shift on the different excited states can be considered assessed. The study of the excited state decay, both radiative and non-radiative, in solution still poses instead significant theoretical challenges. © Springer-Verlag Berlin Heidelberg 2014.


Improta R.,CNR Institute of Biostructure and Bioimaging
Journal of Physical Chemistry B | Year: 2012

We here report a fully quantum mechanical study of the main photochemical and photophysical decay routes in aqueous solution of thymine deoxy-dinucleotide (TpT- and TpTNa) and of its analogue locked in C3-endo puckering, characterizing five different representative backbone conformers and discussing the chemical physical effects modulating the yield of the different photoproducts. Our approach is based on time-dependent DFT calculations, using the last generation M052X functional, whereas solvent effects are included by means of the polarizable continuum model. Especially when at least one of the sugars adopts C3-endo puckering, a barrierless path on the bright ππ* excitons leads to the S1/S0 crossing region corresponding to the formation of cyclobutane pyrimidine dimer. Charge transfer excited states involving the transfer of an electron from the 5′ Thy toward the 3′ Thy are involved in the formation of the oxetane intermediate in the path leading to 6-4 pyrimidine pyrimidinone adducts. A non-negligible energy barrier is associated with this latter pathway, which is possible only when one of the two nucleotides adopts C2-endo puckering. Monomer-like decay pathways, involving ππ* or nπ* excited states localized on a single base, are shown to be operative also for loosely stacked bases. © 2012 American Chemical Society.


Improta R.,CNR Institute of Biostructure and Bioimaging
Chemistry - A European Journal | Year: 2014

Herein, a full quantum mechanical study, in solution, of several models of guanine-quadruplex helices, both parallel and antiparallel, containing up to eight guanine residues, in their electronic excited state is reported. By exploiting TD-DFT calculations and including solvent effects by the polarizable continuum model, we provide the first atomistic description of the processes triggered by the absorption of UV light, reproducing and assigning the experimental optical and electronic circular dichroism spectra. The absorbing excited states are delocalized over multiple bases, whereas emission involves a stacked guanine dimer or a monomer. Several states, with a varying degree of localization and charge-transfer character, rule the photoexcited dynamics, which are deeply affected by the quadruplex topology. The lowest excited-state minimum for parallel quadruplex is an asymmetric excimer involving two stacked guanines, with a small charge transfer character, whereas for the anti-parallel structure, with the same topology of the thrombin binding aptamer, it is a fully symmetric excimer, characterized by a strong decrease of the stacking distance. A monomer-like decay path is the most relevant nonradiative decay pathway. Insights on the effect of the ions (K+ or Na+) on the excited state decay are also provided. Shedding light on quadruple helices: Quantum mechanical calculations show what happens when a guanine quadruplex absorbs UV radiation, allowing the assignment of the absorption and fluorescence spectra and giving insights into the factors ruling their photoexcited behavior (see figure). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.


Improta R.,CNR Institute of Biostructure and Bioimaging | Vitagliano L.,CNR Institute of Biostructure and Bioimaging | Esposito L.,CNR Institute of Biostructure and Bioimaging
Acta Crystallographica Section D: Biological Crystallography | Year: 2015

By combining quantum-mechanical analysis of small model peptides and statistical surveys of high-resolution protein structures, a systematic conformational dependence of bond lengths in polypeptide backbones has been unveiled which involves both the peptide bond (C-O and C-N) and those bonds centred on the Cα atom. All of these bond lengths indeed display a systematic variability in the ψ angle according to both calculations and surveys of protein structures. The overall agreement between the computed and the statistical data suggests that these trends are essentially driven by local effects. The dependence of Cα distances on ψ is governed by interactions between the σ system of the Cα moiety and the C-O π system of the peptide bond. Maximum and minimum values for each bond distance are found for conformations with the specific bond perpendicular and parallel to the adjacent CONH peptide plane, respectively. On the other hand, the variability of the C-O and C-N distances is related to the strength of the interactions between the lone pair of the N atom and the C-O π∗ system, which is modulated by the ψ angle. The C-O and C-N distances are related but their trends are not strictly connected to peptide-bond planarity, although a correlation amongst all of these parameters is expected on the basis of the classical resonance model. © 2015 International Union of Crystallography.

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