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Binding ability of Zn(ii) complexes of [9]aneN3-based receptors for selective recognition of glyphosate in aqueous media.

The research on new radiopharmaceuticals for therapy of cancer is evolving rapidly. Thanks to novel technologies and new selective and less toxic compounds, we move towards personalized molecular medicine. The neutron capture radiation therapy (NCT) can be potentially much safer and can offer a better spatial and temporal control than the radioisotope therapy. Still, there are not many options in NCT: the 10B isotope has been almost exclusively used for decades, and only recently, 157Gd has attracted some interest. Here, we want to draw attention to a new nuclide, 7Be, recently suggested for the NCT, and discuss perspective of Be2+ confinement in aqueous solutions and targeted delivery to cancerous tissues.

In this work, industrial waste hexafluorosilicic acid (H2SiF6 or FSA) has been proven to be a low-cost alternative to silicate esters for the synthesis of high-quality MCM-41 (high surface area, hi...

The synthesis and coordination properties of two fluorescent chemosensors, featuring [9]aneN3 (1,4,7-triazacyclononane; L1) and [12]aneNS3 (1-aza-4,7,10-trithiacyclododecane; L2) as receptor units, and a quinoline pendant arm with an amide group as a functional group spacer are described. The optical responses of L1 and L2 in the presence of several metal ions were analysed in MeCN/H2 O (1 : 4 v/v) solutions. A selective chelation enhancement of fluorescence (CHEF) effect was observed in the presence of Zn2+ in the case of L1, and in the presence of Cd2+ in the case of L2, following the formation of a 1 : 1 and a 1 : 2 metal/ligand complex, respectively, which was also confirmed by potentiometric measurements. 1 H and 13 C NMR measurements in CD3 CN/CDCl3 in combination with molecular mechanics calculations show that for both complexes of L1 and L2 with Zn2+ and Cd2+ , respectively, the coordination of the carbonyl group from the pendant arm could be the origin of the observed optical selectivity.

The study investigates conformational analysis and the in vitro cytokine-mediated immunomodulatory and insulin-releasing activities of rhinophrynin-27 (ELRLPEIARPVPEVLPARLPLPALPRN; RP-27), a proline-arginine-rich peptide first isolated from skin secretions of the Mexican burrowing toad Rhinophrynus dorsalis (Rhinophrynidae). In both water and 50% trifluoroethanol-water, the peptide adopts a polyproline type II helical conformation with a high degree of deviation from the canonical collagen-like folding and a pronounced bend in the molecule at the Glu13 residue. Incubation of mouse peritoneal cells with RP-27 significantly (P

We describe here the synthesis and coordination properties of three new derivatives of [9]aneN3 containing phenyl/quinoline pendant arm derivatives (L1, L2 and L3, respectively) also featuring urea (L1–L2) or amide (L3) functions as “non-innocent” spacers. At first, L1, L2 and L3 were studied considering the interaction with a series of anions (AcO−, BzO−, H2PO4−, F−, and Cl−) by means of 1H NMR measurements. Subsequently, the optical responses of L2 and L3 in the presence of several metal ions Cd2+, Co2+, Cu2+, Fe3+, Hg2+, K+, Mg2+, Mn2+, Ni2+, Zn2+ and Pb2 were analysed in MeCN/H2O (4 : 1 v/v). As observed by spectrophotometric and spectrofluorimetric titrations, there were significant changes in the absorbance and fluorescent emission of L2 upon addition of increasing amounts of Cd2+, Zn2+, Pb2+ and Cu2+ in MeCN/H2O (4 : 1 v/v). In particular, titrations of L2 with Cd2+, Zn2+ or Pb2+ showed an almost comparable CHEF effect up to an M2+/L2 molar ratio of 1. Overall, no significant optical selectivity was observed in the case of L2. Conversely, L3 revealed an OFF–ON selective response only in the presence of the Zn2+ ion in MeCN/H2O (4 : 1 v/v), which can be attributed to the formation of both 1 : 1 and 1 : 2 metal-to-ligand complexes, as also confirmed by potentiometric measurements. Finally, crystals of [ZnL1(Ac)](Ac) (1), [CuL1(Cl)](Cl)·H2O (2) and [CuL3](NO3) (3) were grown and analysed by X-ray diffraction. 1 and 3 feature the metal center in a pseudo-octahedral coordination geometry coordinated also by the carbonyl group from one pendant arm, while in the case of 2, one of the six coordination sites in the final distorted octahedral geometry is occupied by the nitrogen donor from the urea group of one pendant arm.

The research on new radiopharmaceuticals for therapy of cancer is evolving rapidly. Thanks to novel technologies and new selective and less toxic compounds, we move towards personalized molecular medicine. The neutron capture radiation therapy (NCT) can be potentially much safer and can offer a better spatial and temporal control than the radioisotope therapy. Still, there are not many options in NCT: the

Modern medicine relies upon antibiotics, but we have arrived to the point where our inability to come up with new effective molecules against resistant pathogens, together with the declining private investment, is resulting in the number of untreatable infections increasing worldwide at worrying pace. Among other pathogens, widely recognized institutions have indicated Gram-negative bacteria as particularly challenging, due to the presence of the outer membrane. The very first step in the action of every antibiotic or adjuvant is the permeation through this membrane, with small hydrophilic drugs usually crossing through protein channels. Thus, a detailed understanding of their properties at a molecular level is crucial. By making use of Molecular Dynamics simulations, we compared the two main porins of four members of the Enterobacteriaceae family, and, in this paper, we show their shared geometrical and electrostatic characteristics. Then, we used metadynamics simulations to reconstruct the free energy for permeation of selected diazobicyclooctans through OmpF. We demonstrate how porins features are coupled to those of the translocating species, modulating their passive permeation. In particular, we show that the minimal projection area of a molecule is a better descriptor than its molecular mass or the volume. Together with the magnitude and orientation of the electric dipole moment, these are the crucial parameters to gain an efficient compensation between the entropic and enthalpic contributions to the free energy barrier required for permeation. Our results confirm the possibility to predict the permeability of molecules through porins by using a few molecular parameters and bolster the general model according to which the free energy increase is mostly due to the decrease of conformational entropy, and this can be compensated by a favorable alignment of the electric dipole with respect to the channel intrinsic electric field.

Impressive work has been completed in recent decades on the transmembrane anion transport capability of small synthetic transporters from many different structural classes. However, very few predicting models have been proposed for the fast screening of compound libraries before spending time and resources on the laboratory bench for their synthesis. In this work, a new approach is presented which aims at describing the transport process by taking all the steps into explicit consideration, and includes all possible experiment-derived parameters. The algorithm is able to simulate the macroscopic experiments performed with lipid vesicles to assess the ion-transport ability of the synthetic transporters following a non-electrogenic uniport mechanism. While keeping calculation time affordable, the final goal is the curve-fitting of real experimental data—so, to obtain both an analysis and a predictive tool. The role and the relative weight of the different parameters is discussed and the agreement with the literature is shown by using the simulations of a virtual benchmark case. The fitting of real experimental curves is also shown for two transporters of different structural type., This research was funded by the University of Cagliari (FIR 2020). Financial support from MIUR (PRIN 2017 project 2017EKCS35), Fondazione di Sardegna (FdS Progetti Biennali di Ateneo, annualità 2018 and 2020) is also gratefully acknowledged.

Voltage-dependent anion-selective channels (VDACs) are primarily located in the mitochondrial outer membrane (MOM). They are essential for the regulation of ion and metabolite exchanges. In particular, their role in energy-related nucleotide exchange has many implications in apoptosis, cancer, and neurodegenerative diseases. It has been proposed that VDACs' functions are regulated by mobility of the N-terminal helical domain, which is bound to the inner wall of the main β-barrel domain but exists in equilibrium between the bound-folded and the unbound-unfolded state. When the N-terminal domain detaches from the channel's wall and eventually leaves the lumen, it can either stay exposed to the cytosolic environment or interact with the outer leaflet of the MOM; then, it may also interact with other protein partners. In humans, three different VDAC isoforms are expressed at different tissue-specific levels with evidence of distinct roles. Although the N-terminal domains share high sequence similarity, important differences do exist, with the functionality of the entire protein mostly attributed to them. In this work, the three-dimensional structure and membrane affinity of the three isolated hVDAC N-terminal peptides have been compared through Fourier-transform infrared and NMR spectroscopy in combination with molecular dynamics simulations, and measurement of the surface pressure of lipid monolayers. Although peptides were studied as isolated from the β-barrel domain, the observed differences are relevant for those whole protein's functions in which a protein-protein interaction is mediated by the N-terminal domain.

Antimicrobial peptides attracted increasing interest in last decades due to the rising concern of multi-drug resistant pathogens. Dendrimeric peptides are branched molecules with multiple copies of one peptide functional unit bound to the central core. Compared to linear analogues, they usually show improved activity and lower susceptibility to proteases. Knowledge of structure-function relationship is fundamental to tailor their properties. This work is focused on SB056, the smallest example of dendrimeric peptide, whose amino acid sequence is WKKIRVRLSA. Two copies are bound to the α- and e- nitrogen of one lysine core. An 8-aminooctanamide was added at the C-terminus to improve membrane affinity. Its propensity for β-type structures is also interesting, since helical peptides were already thoroughly studied. Moreover, SB056 maintains activity at physiological osmolarity, a typical limitation of natural peptides. An optimized analogue with improved performance was designed, β-SB056, which differs only in the relative position of the first two residues (KWKIRVRLSA). This produced remarkable differences. Structure order and aggregation behavior were characterized by using complementary techniques and membrane models with different negative charge. Infrared spectroscopy showed different propensity for ordered β-sheets. Lipid monolayers’ surface pressure was measured to estimate the area/peptide and the ability to perturb lipid packing. Fluorescence spectroscopy was applied to compare peptide insertion into the lipid bilayer. Such small change in primary structure produced fundamental differences in their aggregation behavior. A regular amphipathic peptide’s primary structure was responsible for ordered β-sheets in a charge independent fashion, in contrast to unordered aggregates formed by the former analogue.

A green, one-pot approach based on the solvothermal amidation of carboxylic acids with amines has been developed for the synthesis of diverse aliphatic and aromatic amides. It does not require the use of catalysts or coupling reagents and it occurs in the presence of ethanol that has been proved to have a key role in the process. The proposed strategy is also extendable to biologically active amides and could represent a low-cost and waste-less alternative to the common synthetic pathways.

NiP alloys are very often used in industry, due to their outstanding performance in corrosion and wear. Alloys with high phosphorus content (≥16 atom % P) are amorphous and show high corrosion resistance in both neutral and acidic solutions irrespective of the presence of chloride ions. The reason for this behavior is attributed to the formation of a “P-enriched surface layer” whose exact nature is still under debate. In this work, an iterative algorithm based on the application of maximum entropy method on nondestructive angle-resolved X-ray photoelectron spectroscopy data has been applied to the investigation of the surface layer grown on Ni18P alloys following mechanical polishing and anodic polarization in sulfate solutions. The results show that the outermost region of the examined alloy has a complex layered structure: (1) an uppermost hydrocarbon contamination layer about 1 nm thick, which includes also adsorbed water; (2) a nickel (poly)phosphate layer of about 1 nm; (3) a highly phosphorus-enriched interface being about 2 nm thick with a marked phosphorus concentration gradient, from 70 to 20 atom %; and (4) bulk alloy with the stoichiometric composition. These findings, together with the chemical state of the different phosphorus compounds, allow us to conclude that the high corrosion and wear resistance of NiP alloys might be ascribed to the presence of a thin, self-repairing nickel (poly)phosphate layer grown on a strongly P-enriched interface. Because the Auger parameter of P at the interface is similar to that of elemental P, it might be also concluded that the interface is enriched in elemental phosphorus., ACS Omega, 2 (11), ISSN:2470-1343

A major challenge in the discovery of the new antibiotics against Gram-negative bacteria is to achieve sufficiently fast permeation in order to avoid high doses causing toxic side effects. So far, suitable assays for quantifying the uptake of charged antibiotics into bacteria are lacking. We apply an electrophysiological zero-current assay using concentration gradients of β-lactamase inhibitors combined with single-channel conductance to quantify their flux rates through OmpF. Molecular dynamic simulations provide in addition details on the interactions between the nanopore wall and the charged solutes. In particular, the interaction barrier for three β-lactamase inhibitors is surprisingly as low as 3-5 kcal/mol and only slightly above the diffusion barrier of ions such as chloride. Within our macroscopic constant field model, we determine that at a zero-membrane potential a concentration gradient of 10 μM of avibactam, sulbactam, or tazobactam can create flux rates of roughly 620 molecules/s per OmpF trimer.

Nuclear magnetic resonance and infrared spectroscopy have been used to investigate the formation of complexes of BAL30072 with Fe3+ and Ga3+ in solution and to collect geometrical parameters supporting reliable 3D structure models. Structural models for the ligand-metal complexes with different stoichiometries have been characterized using density functional theory calculations. Blind ensemble docking to the PiuA receptor from P. aeruginosa was performed for the different complexes to compare binding affinities and statistics of the residues most frequently contacted. When compared to analogues, BAL30072 was found to have an intrinsic propensity to form complexes with low ligand-to-metal stoichiometry. By using one of the sulfate oxygen atoms as a third donor in addition to the bidentate pyridinone moiety, BAL30072 can form a L2M complex, which was predicted to be the one with the best binding affinity to PiuA. The example of BAL30072 strongly suggests that a lower stoichiometry might be the one recognized by the receptor, so that to focus only on the highest stoichiometry might be misleading for siderophores with less than six donors.

We describe here the synthesis and coordination properties of three new derivatives of [9]aneN3 containing phenyl/quinoline pendant arm derivatives (L1, L2 and L3, respectively) also featuring urea (L1-L2) or amide (L3) functions as "non-innocent" spacers. At first, L1, L2 and L3 were studied considering the interaction with a series of anions (AcO-, BzO-, H2PO4-, F-, and Cl-) by means of 1H NMR measurements. Subsequently, the optical responses of L2 and L3 in the presence of several metal ions Cd2+, Co2+, Cu2+, Fe3+, Hg2+, K+, Mg2+, Mn2+, Ni2+, Zn2+ and Pb2 were analysed in MeCN/H2O (4 : 1 v/v). As observed by spectrophotometric and spectrofluorimetric titrations, there were significant changes in the absorbance and fluorescent emission of L2 upon addition of increasing amounts of Cd2+, Zn2+, Pb2+ and Cu2+ in MeCN/H2O (4 : 1 v/v). In particular, titrations of L2 with Cd2+, Zn2+ or Pb2+ showed an almost comparable CHEF effect up to an M2+/L2 molar ratio of 1. Overall, no significant optical selectivity was observed in the case of L2. Conversely, L3 revealed an OFF-ON selective response only in the presence of the Zn2+ ion in MeCN/H2O (4 : 1 v/v), which can be attributed to the formation of both 1 : 1 and 1 : 2 metal-to-ligand complexes, as also confirmed by potentiometric measurements. Finally, crystals of [ZnL1(Ac)](Ac) (1), [CuL1(Cl)](Cl)·H2O (2) and [CuL3](NO3) (3) were grown and analysed by X-ray diffraction. 1 and 3 feature the metal center in a pseudo-octahedral coordination geometry coordinated also by the carbonyl group from one pendant arm, while in the case of 2, one of the six coordination sites in the final distorted octahedral geometry is occupied by the nitrogen donor from the urea group of one pendant arm.

Four host-defense peptides belonging to the tigerinin family (tigerinin-1O: RICTPIPFPMCY; tigerinin-2O: RTCIPIPLVMC; tigerinin-3O: RICTAIPLPMCL; and tigerinin-4O: RTCIPIPPVCF) were isolated from skin secretions of the African crowned bullfrog Hoplobatrachus occipitalis. In aqueous solution at pH 4.8, the cyclic domain of tigerinin-2O adopts a rigid amphipathic conformation that incorporates a flexible N-terminal tail. The tigerinins lacked antimicrobial (MIC100 μM) and hemolytic (LC50500 μM) activities but, at a concentration of 20 μg/mL, significantly (P0.05) inhibited production of interferon-γ (IFN-γ) by peritoneal cells from C57BL/6 mice without affecting production of IL-10 and IL-17. Tigerinin-2O and -4O inhibited IFN-γ production at concentrations as low as 1 μg/mL. The tigerinins significantly (P ≤ 0.05) stimulated the rate of insulin release from BRIN-BD11 clonal β-cells without compromising the integrity of the plasma membrane. Tigerinin-1O was the most potent (threshold concentration 1 nM) and the most effective (395% increase over basal rate at a concentration of 1 μM). Tigerinin-4O was the most potent and effective peptide in stimulating the rate of glucagon-like peptide-1 release from GLUTag enteroendocrine cells (threshold concentration 10 nM; 289% increase over basal rate at 1 μM). Tigerinin peptides have potential for development into agents for the treatment of patients with type 2 diabetes.

Background: In Gram-negative bacteria, the outer-membrane represents an additional barrier for antibiotics to permeate inside pathogens. Our inability to come up with novel effective antibiotics mostly relies upon insufficient understanding of the molecular basis behind outer-membrane penetration. Results: Polar antibiotics can permeate through water-filled porins, such as OmpF and OmpC from Escherichia coli. Through molecular modeling, permeation of imipenem and meropenem was found to be strongly dependent upon capability of drugs to properly align their electric dipole to the internal electric field in the restricted region of the pore. Electrostatics differences between OmpF and OmpC, and modifications along a series of OmpC mutants from E. coli-resistant clinical strains identify a ‘preorientation’ region, which dramatically affects antibiotic pathway. Conclusion: A novel perspective is presented, suggesting new molecular properties to be included in drug design.

The fluorescent ligand (L) based on the N2S2 pyridinophane macrocycle and the 7-nitrobenzo[1,2,5]oxadiazole (NBD) fluorogenic fragment has been synthesized to coordinate Pd(II) ions. Loaded on dye-doped silica nanoparticles, L can be used as a ratiometric fluorescent chemosensor for Pd(II) in water with high selectivity toward other metal ions including the platinum group ones.

Integral membrane proteins known as porins are the major pathway by which hydrophilic antibiotics cross the outer membrane of Gram-negative bacteria. Single point mutations in porins can decrease the permeability of an antibiotic, either by reduction of channel size or modification of electrostatics in the channel, and thereby confer clinical resistance. Here, we investigate four mutant OmpC proteins from four different clinical isolates of Escherichia coli obtained sequentially from a single patient during a course of antimicrobial chemotherapy. OmpC porin from the first isolate (OmpC20) undergoes three consecutive and additive substitutions giving rise to OmpC26, OmpC28, and finally OmpC33. The permeability of two zwitterionic carbapenems, imipenem and meropenem, measured using liposome permeation assays and single channel electrophysiology differs significantly between OmpC20 and OmpC33. Molecular dynamic simulations show that the antibiotics must pass through the constriction zone of porins with a specific orientation, where the antibiotic dipole is aligned along the electric field inside the porin. We identify that changes in the vector of the electric field in the mutated porin, OmpC33, create an additional barrier by "trapping" the antibiotic in an unfavorable orientation in the constriction zone that suffers steric hindrance for the reorientation needed for its onward translocation. Identification and understanding the underlying molecular details of such a barrier to translocation will aid in the design of new antibiotics with improved permeation properties in Gram-negative bacteria.

// Simona Reina 1,2* , Vanessa Checchetto 3,4,5,* , Rosaria Saletti 6 , Ankit Gupta 7,* , Deepti Chaturvedi 7,* , Carlo Guardiani 8 , Francesca Guarino 1,2 , Mariano Andrea Scorciapino 9 , Andrea Magri 1,2 , Salvatore Foti 6 , Matteo Ceccarelli 8,10,** , Angela Anna Messina 11,12,** , Radhakrishnan Mahalakshmi 7,** , Ildiko Szabo 3,4,** and Vito De Pinto 1,2 1 Department of Biomedicine and Biotechnology BIOMETEC, Section of Biology and Genetics, University of Catania, Catania, Italy 2 National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy 3 Department of Biology, University of Padova, Padova, Italy 4 CNR Institute of Neurosciences, Padova, Italy 5 Department of Biomedical Sciences, University of Padova, Padova, Italy 6 Department of Chemical Sciences, Mass Spectrometry Unit, University of Catania, Catania, Italy 7 Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India 8 Department of Physics, University of Cagliari, Cagliari, Italy 9 Department of Biomedical Sciences, Biochemistry Unit, University of Cagliari, Cagliari, Italy 10 Istituto Officina dei Materiali del Consiglio Nazionale delle Ricerche (IOM-CNR), UOS, Trieste, Italy 11 Department of Biological, Geological and Environmental Sciences, Section of Molecular Biology, University of Catania, Catania, Italy 12 National Institute for Biomembranes and Biosystems, Section of Catania, Catania, Italy * These authors have contributed equally to this work ** Co-corresponding author Correspondence to: Vito De Pinto, email: // Keywords : VDACs, cysteine oxidation, disulfide bridge, mitochondrial intermembrane space, mass spectrometry Received : October 21, 2015 Accepted : December 23, 2015 Published : January 08, 2016 Abstract Voltage-Dependent Anion selective Channels (VDAC) are pore-forming mitochondrial outer membrane proteins. In mammals VDAC3, the least characterized isoform, presents a set of cysteines predicted to be exposed toward the intermembrane space. We find that cysteines in VDAC3 can stay in different oxidation states. This was preliminary observed when, in our experimental conditions, completely lacking any reducing agent, VDAC3 presented a pattern of slightly different electrophoretic mobilities. This observation holds true both for rat liver mitochondrial VDAC3 and for recombinant and refolded human VDAC3. Mass spectroscopy revealed that cysteines 2 and 8 can form a disulfide bridge in native VDAC3. Single or combined site-directed mutagenesis of cysteines 2, 8 and 122 showed that the protein mobility in SDS-PAGE is influenced by the presence of cysteine and by the redox status. In addition, cysteines 2, 8 and 122 are involved in the stability control of the pore as shown by electrophysiology, complementation assays and chemico-physical characterization. Furthermore, a positive correlation between the pore conductance of the mutants and their ability to complement the growth of porin-less yeast mutant cells was found. Our work provides evidence for a complex oxidation pattern of a mitochondrial protein not directly involved in electron transport. The most likely biological meaning of this behavior is to buffer the ROS load and keep track of the redox level in the inter-membrane space, eventually signaling it through conformational changes.

New strategies are urgently required to develop antibiotics. The siderophore uptake system has attracted considerable attention, but rational design of siderophore antibiotic conjugates requires knowledge of recognition by the cognate outer-membrane transporter. Acinetobacter baumannii is a serious pathogen, which utilizes (pre)acinetobactin to scavenge iron from the host. We report the structure of the (pre)acinetobactin transporter BauA bound to the siderophore, identifying the structural determinants of recognition. Detailed biophysical analysis confirms that BauA recognises preacinetobactin. We show that acinetobactin is not recognised by the protein, thus preacinetobactin is essential for iron uptake. The structure shows and NMR confirms that under physiological conditions, a molecule of acinetobactin will bind to two free coordination sites on the iron preacinetobactin complex. The ability to recognise a heterotrimeric iron-preacinetobactin-acinetobactin complex may rationalize contradictory reports in the literature. These results open new avenues for the design of novel antibiotic conjugates (trojan horse) antibiotics.

Although the role of general bacterial porins is well established as main pathway for polar antibiotics, the molecular details of their mode-of-action are still under debate. Using molecular dynamics simulations and water as a probe, we demonstrated the strong ordering of water molecules, differently tuned along the axis of diffusion in the transversal direction. Preserved features and important differences were characterized for different channels, allowing to put forward a general model for molecular filtering. The intrinsic electric field, responsible for water ordering, (i) filters those dipolar molecules that can compensate the entropy decrease by dipole alignment in the restricted region and (ii) might create an additional barrier by changing direction when escaping from the restricted region. We tested this model using two antibiotics, cefepime and cefotaxime, through metadynamics free energy calculations. A rational drug design should take this into account for screening molecules with improved permeation properties.

An ecofriendly, low-cost, one-pot solvothermal approach has been developed to prepare spherical magnetite nanoparticles with sizes in the 7–12 nm range capped with a dialkylamine. Iron isopropoxide, water vapor, absolute ethanol, oleic acid, and oleylamine were used as iron oxide precursor, hydrolysis agent, solvent and surfactants, respectively. The surfactants’ role was investigated and an accurate correlation among the synthetic parameters, the crystallographic phases, and both crystallite and particle size was found. The amounts of oleylamine and oleic acid and the temperature have been revealed to be the key parameters in order to tune particle size and their polydispersity. An in-depth study on the role of each surfactant has pointed out the fundamental role of the amine as a reduction promoter as demonstrated by using different amines and confirmed by Mossbauer measurements. A dual 1H NMR-Fourier transform infrared spectroscopy approach on selected experiments for the investigation of the capping a...

The objective of this study is to identify the structural features governing the transport of molecules through nanometric channel proteins at a molecular level. Our focus is to come up with a precise understanding of the structure and dynamics of the outer membrane porin OprD of the Gram-negative bacterium Pseudomonas aeruginosa by studying the translocation of natural amino acid residues/substrates through it. We used in silico electrophysiology and metadynamics simulation techniques as they can provide precise information on the molecule/channel interactions at the atomic scale that allows testing quantitative structure-function relationships. We performed our simulations on the whole OprD protein, with all loops modelled and without any constraints to keep the channel open. Dynamics of both internal and external loops and the polar nature of the eyelet region play important roles in modulating the translocation of molecules through OprD by creating two alternative paths for translocation. All positive residues take the main path upon binding in the negative pocket just above the constriction region. The same factor is unfavourable for negative substrates and hence they have a relatively high barrier for translocation. Differently, neutral substrates do not show any specificity and they can follow the two alternative paths.

Pseudomonas aeruginosa is a major cause of chronic lung infections in cystic fibrosis (CF) patients. The ability of the bacterium to form biofilms and the presence of a thick and stagnant mucus in the airways of CF patients largely contribute to antibiotic therapy failure and demand for new antimicrobial agents able to act in the CF environment. The present study investigated the anti-P. aeruginosa activity of lin-SB056-1, a recently described semi-synthetic antimicrobial peptide, used alone and in combination with the cation chelator ethylenediaminetetraacetic acid (EDTA). Bactericidal assays were carried out in standard culture conditions and in an artificial sputum medium (ASM) closely resembling the CF environment. Peptide’s structure and interaction with large unilamellar vesicles in media with different ionic strengths were also investigated through infrared spectroscopy. Lin-SB056-1 demonstrated fast and strong bactericidal activity against both mucoid and non-mucoid strains of P. aeruginosa in planktonic form and, in combination with EDTA, caused significant reduction of the biomass of P. aeruginosa mature biofilms. In ASM, the peptide/EDTA combination exerted a strong bactericidal effect and inhibited the formation of biofilm-like structures of P. aeruginosa. Overall, the results obtained highlight the potential of the lin-SB056-1/EDTA combination for the treatment of P. aeruginosa lung infections in CF patients.

Transport of molecules through biological membranes is a fundamental process in biology, facilitated by selective channels and general pores. The architecture of some outer membrane pores in Gram-negative bacteria, common to other eukaryotic pores, suggests them as prototypes of electrostatically regulated nanosieve devices. In this study, we sensed the internal electrostatics of the two most abundant outer membrane channels of Escherichia coli, using norfloxacin as a dipolar probe in single molecule electrophysiology. The voltage dependence of the association rate constant of norfloxacin interacting with these nanochannels follows an exponential trend, unexpected for neutral molecules. We combined electrophysiology, channel mutagenesis, and enhanced sampling molecular dynamics simulations to explain this molecular mechanism. Voltage and temperature dependent ion current measurements allowed us to quantify the transversal electric field inside the channel as well as the distance where the applied potential drops. Finally, we proposed a general model for transport of polar molecules through these electrostatic nanosieves. Our model helps to further understand the basis for permeability in Gram-negative pathogens, contributing to fill in the innovation gap that has limited the discovery of effective antibiotics in the last 20 years.

Microbial resistance to conventional antibiotics is one of the most outstanding medical and scientific challenges of our times. Despite the recognised need for new anti-infective agents, however, very few new drugs have been brought to the market and to the clinic in the last three decades. This review highlights the properties of a new class of antibiotics, namely dendrimeric peptides. These intriguing novel compounds, generally made of multiple peptidic sequences linked to an inner branched core, display an array of antibacterial, antiviral and antifungal activities, usually coupled to low haemolytic activity. In addition, several peptides synthesized in oligobranched form proved to be promising tools for the selective treatment of cancer cells.

The demand of new drugs for combating multidrug-resistant bacteria appears more urgent for Gram-negative bacteria: the presence of the outer membrane, which hinders the access of molecules to internal targets, renders the development of anti-infectives more challenging. Today neither a robust screening method for permeation nor defined physical/chemical rules governing permeation through the outer membrane are available. By assuming diffusion as the physical mechanism of the transport of molecules through the channels, we suggest a simple quantitative model for the free energy profile of the molecule-pore interaction.

This work presents an in-depth investigation of the molecular interactions in the incorporation mechanism of colloidal hydrophobic-capped nanoparticles into the hydrophilic core of reverse microemulsions. (1)H Nuclear Magnetic Resonance (NMR) was employed to obtain molecular level details of the interaction between the nanoparticles capping amphiphiles and the microemulsion surfactants. The model system of choice involved oleic acid (OAC) and oleylamine (OAM) as capping molecules, while igepal-CO520 was the surfactant. The former were studied both in their "free" state and "ligated" one, i.e., bound to nanoparticles. The latter was investigated either in cyclohexane (micellar solution) or in water/cyclohexane microemulsions. The approach was extremely useful to gain a deeper understanding of the equilibria involved in this complex system (oleic acid capped-Bi2S3 in igepal/water/cyclohexane microemulsions). In difference to previously proposed mechanisms, the experimental data showed that the high affinity of the capping ligands for the reverse micelle interior was the drivingforce for the incorporation of the nanoparticles. A simple ligand-exchange mechanism could be ruled out. The collected information about the nanoparticle incorporation mechanism is extremely useful to develop new synthetic routes with an improved/tuned coating efficiency, in order to tailor the core-shell structure preparation.

The complexity of biological membranes leads to the use of extremely simplified models in biophysical investigations of membrane-bound proteins and peptides. Liposomes are probably the most widely used membrane models due, especially, to their versatility in terms of electric charge and size. However, liquid-state NMR suffers the lack of such a model, because even the smallest liposomes slowly tumble in solution, resulting in a dramatic signals broadening. Micelles are typically used as good substitutes, with sodium dodecylsulphate (SDS) and dodecylphosphocholine (DPC) being the most widely employed surfactants. However, they are always used separately to mimic prokaryotic and eukaryotic membranes, respectively, and accurate investigations as a function of surface charge cannot be performed. In this work, the critical micelle concentration (CMC) of binary mixtures with different SDS/DPC ratios has been determined by following the chemical shift variation of selected (1)H and (31)P NMR signals as a function of total surfactant concentration. The regular solution theory and the Motomura's formalism have been applied to characterize the micellization both in water and in phosphate buffer saline, and results were compared with those obtained directly from the experimental NMR chemical shift. The ζ-potential and size distribution of the mixed micelles have been estimated with dynamic light scattering measurements. Results showed that SDS and DPC are synergic and can be used together to prepare mixed micelles with different negative/zwitterionic surfactants molar ratio.

Multi-drug resistance bacteria are a challenging problem of contemporary medicine. This is particularly critical for Gram-negative bacteria, where antibiotics are hindered by the outer membrane to reach internal targets. Here more polar antibiotics make use of nanometric water-filled channels to permeate inside. We present in this work a computational all-atom approach, using water as a probe, for the calculation of the macroscopic electric field inside water-filled channels. The method allows one to compare not only different systems but also the same system under different conditions, such as pH and ion concentration. This provides a detailed picture of electrostatics in biological nanopores shedding more light on how the charged residues of proteins determine the electric field inside, and also how medium can tune it. These details are central to unveil the filtering mechanism behind the permeation of small polar molecules through nanometric water-filled channels.

Three fluorescent asymmetric bis-urea receptors (L1-L3) have been synthesised. The binding properties of L1-L3 towards different anions (fluoride, acetate, hydrogencarbonate, dihydrogen phosphate, and hydrogen pyrophosphate HPpi(3-)) have been studied by means of (1)H-NMR, UV-Vis and fluorescence spectroscopy, single crystal X-ray diffraction, and theoretical calculations. In particular, a remarkable affinity for HPpi(3-) has been observed in the case L1 (DMSO-d6/0.5% H2O) which also acts as a fluorimetric chemosensor for this anion. Interestingly, when L1 is included in cetyltrimethylammonium (CTAB) micelles, hydrogen pyrophosphate recognition can also be achieved in pure water.

The accumulation in mitochondria of oxidative agents must be signaled to the cell. Neverthless the organelle is the source of redox species. The accumulation in mitochondria of oxidative agents must be signaled to the cell and an organelle heavily loaded with ROS evidenced. We addressed specific structural questions related to the function of VoltageDependentAnion-selectiveChannel isoform 3 (VDAC3) cysteines. We show that VDAC3 (1–3) may be relevant for signaling the redox potential existing in the mitochondrial intermembrane space. We found that VDAC3 can be progressively modified by an accumulation of ROS, resulting in the oxidation at different extents of the exposed cysteine residues. We discovered that each single VDAC3 molecule in the membrane can contain a differently oxidated set of cysteine residues, thus giving rise to what we call “redox isomers” (4). A disulfide bridge was evidenced by mass spectrometry (5). A recent paper indicated a putative disulfide bridge that we did not find by MassSpec (6), neither the authirs detected intermediate oxidation states. Since this complex oxidation pattern is a consequence of the ROS level in the IMS, VDAC3 monitores the redox homeostasis. In our opinion this work represents a pathbreaking finding in the field of mitochondrial redox sensing.Acknowledgements MIUR-PRIN 2010-2011 n. 2010CSJX4F[1] Messina A. et al, 2012, BiochimBiophysActa 1818, 1466-1476[2] Checchetto V. et al, 2014, Cell Physiol. Biochem. 34, 842-53[3] Messina A. et al, 2014, Mol. Biosyst. 10, 2134-45[4] Reina S. et al 2015, SUBMITTED[5] Saletti R. et al, 2015, SUBMITTED[6] Okazaki M. et al, 2015, BiochimBiophysActa, in press

The number of multiple drug resistant pathogens is ever increasing. The impact on healthcare systems is urgently demanding for novel classes of antibiotics, especially against Gram-negative bacteria. Their first line of defense is the outer membrane, where unspecific protein channels, called porins, modulate passive diffusion of nutrients. Porins are considered today the main path for entry of polar antibiotics into the bacterial cell. Down-regulation and/or mutation of porins are very common in drug resistant strains.1 The inability to come up with novel effective antibiotics mostly relies upon the insufficient comprehension of the key molecular features for better penetration. This can be obtained with molecular dynamics simulations, an atomic level microscope for detailed investigation of molecules’ translocation choreography through protein channels.In this work, a series of unspecific porins were selected, including also clinical mutant isolates. As their size is comparable1, structural comparison was focused on lumen electrostatics. Serial modifications of the internal electric field was found moving from wild-type porins to resistant mutants. Water molecules were used as an intrinsic molecular probe and the electric field variations inside the channels matched with charged residues distribution.2 Translocation free energy surface was reconstructed for β-lactams antibiotics from different families with multiple-walkers metadynamics simulations.The choreography followed by the molecular electric dipole was analyzed in terms of spherical coordinates to distinguish the influence of different components of the internal electric field. The direction perpendicular to the channel axis is the most important in the absence of an externally applied voltage. The antibiotic has to fit both shape and electrostatics of the channel constriction region to minimize the main energy barrier to translocation.1Lou et al., PloS ONE 6 (2011) e25825.2Acosta-Gutierrez et al., J. Phys. Chem. Lett. 6 (2015) 1807-1812.

Peptide-based antibiotics might help containing the rising tide of antimicrobial resistance. We developed SB056, a semi-synthetic peptide with a dimeric dendrimer scaffold, active against both Gram-negative and Gram-positive bacteria. Being the mechanism of SB056 attributed to disruption of bacterial membranes, we enhanced the amphiphilic profile of the original, empirically derived sequence [WKKIRVRLSA-NH2] by interchanging the first two residues [KWKIRVRLSA-NH2], and explored the effects of this modification on the interaction of peptide, both in linear and dimeric forms, with model membranes and on antimicrobial activity. Results obtained against Escherichia coli and Staphylococcus aureus planktonic strains, with or without salts at physiological concentrations, confirmed the added value of dendrimeric structure over the linear one, especially at physiological ionic strength, and the impact of the higher amphipathicity obtained through sequence modification on enhancing peptide performances. SB056 peptides also displayed intriguing antibiofilm properties. Staphylococcus epidermidis was the most susceptible strain in sessile form, notably to optimized linear analog lin-SB056-1 and the wild-type dendrimer den-SB056. Membrane affinity of all peptides increased with the percentage of negatively charged lipids and was less influenced by the presence of salt in the case of dendrimeric peptides. The analog lin-SB056-1 displayed the highest overall affinity, even for zwitterionic PC bilayers. Thus, in addition to electrostatics, distribution of charged/polar and hydrophobic residues along the sequence might have a significant role in driving peptide-lipid interaction. Supporting this view, dendrimeric analog den-SB056-1 retained greater membrane affinity in the presence of salt than den-SB056, despite the fact that they bear exactly the same net positive charge.

The human VDAC channel exists in three isoforms characterized by high sequence homology and structural similarity. Yet the function and mode of action of hVDAC3 are still elusive. The presence of six surface cysteines exposed to the oxidizing environment of the mitochondrial inter-membrane space suggests the possible establishment of intramolecular disulfide bonds. Two natural candidates for disulfide bridge formation are Cys2 and Cys8 that, located on the flexible N-terminal domain, can easily come in contact. A third potentially important residue is Cys122 that is close to Cys2 in the homology model of VDAC3. Here we analyzed the impact of SS bonds through molecular dynamics simulations of derivatives of hVDAC3 (dubbed SS-2-8, SS-2-122, SS-8-122) including a single disulfide bond. Simulations showed that in SS-8-122, the fragment 1-7 crosses the top part of the barrel partially occluding the pore and causing a 20% drop of conductance. In order to identify other potential channel-occluding disulfide bonds, we used a set of neural networks and structural bioinformatics algorithms, after filtering with the steric constraints imposed by the 3D-structure. We identified other three species, namely SS-8-65, SS-2-36 and SS-8-36. While the conductance of SS-8-65 and SS-2-36 is about 30% lower than that of the species without disulfide bonds, the conductance of SS-8-36 was 40-50% lower. The results show how VDAC3 is able to modulate its pore size and current by exploiting the mobility of the N-terminal and forming, upon external stimuli, disulfide bridges with cysteine residues located on the barrel and exposed to the inter-membrane space. (C) 2016 Elsevier B.V. All rights reserved.