The Interaction of Small Molecules with Biomolecules

The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental dat…

Cyclometalated Au(III) Complexes for Cysteine Arylation in Zinc Finger Protein Domains: Towards Controlled Reductive Elimination

With the aim of exploiting the use of organometallic species for the efficient modification of proteins through C-atom transfer, the gold-mediated cysteine arylation through a reductive elimination process occurring from the reaction of cyclometalated AuIII C^N complexes with a zinc finger peptide (Cys2His2 type) is here reported. Among the four selected AuIII cyclometalated compounds, the [Au(CCON)Cl2] complex featuring the 2-benzoylpyridine (CCON) scaffold was identified as the most prone to reductive elimination and Cys arylation in buffered aqueous solution (pH 7.4) at 37 °C by high-resolution LC electrospray ionization mass spectrometry. DFT and quantum mechanics/molecular mechanics (Q…

Microscopic interactions between ivermectin and key human and viral proteins involved in SARS-CoV-2 infection

The identification of chemical compounds able to bind specific sites of the human/viral proteins involved in the SARS-CoV-2 infection cycle is a prerequisite to design effective antiviral drugs. Here we conduct a molecular dynamics study with the aim to assess the interactions of ivermectin, an antiparasitic drug with broad-spectrum antiviral activity, with the human Angiotensin-Converting Enzyme 2 (ACE2), the viral 3CLpro and PLpro proteases, and the viral SARS Unique Domain (SUD). The drug/target interactions have been characterized in silico by describing the nature of the non-covalent interactions found and by measuring the extent of their time duration along the MD simulation. Results …

Pyrazole[3,4-d]pyrimidine derivatives loaded into halloysite as potential CDK inhibitors

Uncontrolled cell proliferation is a hallmark of cancer as a result of rapid and deregulated progression through the cell cycle. The inhibition of cyclin-dependent kinases (CDKs) activities is a promising therapeutic strategy to block cell cycle of tumor cells. In this work we reported a new example of nanocomposites based on halloysite nanotubes (HNTs)/pyrazolo[3,4-d]pyrimidine derivatives (Si306 and Si113) as anticancer agents and CDK inhibitors. HNTs/Si306 and HNTs/Si113 nanocomposites were synthesized and characterized. The release kinetics were also investigated. Antitumoral activity was evaluated on three cancer cell lines (HeLa, MDA-MB-231 and HCT116) and the effects on cell cycle ar…

Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses

Guanine quadruplex (G4) structures in the viral genome have a key role in modulating viruses' biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modeling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of the RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.

B-DNA Structure and Stability as Function of Nucleic Acid Composition. Dispersion-Corrected DFT Study of Dinucleoside-Monophosphate Single and Double Strands

actions of the sugar-phosphate skeleton with water; (6) hydrophobic interactions of the DNA cylindrical core, made up by the hydrogen-bonded and stacked nitrogen bases, with the water solvent. Recently, there has been increasing effort in developing and applying quantum chemical methods able to reproduce the structure of native B-DNA and to correctly describe the energy involved in the intrastrand and interstrand noncovalent interactions between the nucleotide monomers. This topic has been approached by both wave function methods and density functional theory. [2] Water solvent and sodium counterions also play an important role in the formation and relative stabilization of the double-helic…

G-quadruplex vs. duplex-DNA binding of nickel(II) and zinc(II) Schiff base complexes

Novel nickel(II) (1) and zinc(II) (2) complexes of a Salen-like ligand, carrying a pyrimidine ring on the N,N' bridge, were synthesized and characterized. Their interaction with duplex and G-quadruplex DNA was investigated in aqueous solution through UV-visible absorption, circular dichroism and viscometry measurements. The results obtained point out that, while the zinc(II) complex does not interact with both duplex and G-quadruplex DNA, the nickel(II) complex 1 binds preferentially to G-quadruplex respect to duplex-DNA, with values of the DNA-binding constants, Kb, 2.6×10(5)M(-1) and 3.5×10(4)M(-1), respectively. Molecular dynamics simulations provided an atomic level model of the top-sta…

Synthesis and structural characterisation of copper(I,II) complexes mimetic of "blue copper" proteins active site

The interaction of native calf thymus DNA with FeIII-dipyrido[3,2-a:2’,3’-c]phenazine

The mono and bis dipyrido[3,2-a:2',3'-c]phenazine (dppz) adducts of iron(III) chloride, i.e. [Fe(dppz)]Cl(3) and [Fe(dppz)(2)]Cl(3), have been synthesized and characterized. The interaction of the Fe(III)dppz hydrolyzed aquo complex with native calf thymus DNA has been monitored as a function of the metal complex-DNA molar ratio, by variable temperature UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results obtained in solution at various ionic strength values give support for a tight intercalative binding of the Fe(III)dppz cation with DNA. In particular, the appearance of induced CD bands, caused by the addition of Fe(III)dppz, indicate the exi…

Circular Dichroism of DNA G-Quadruplexes: Combining Modeling and Spectroscopy To Unravel Complex Structures

We report on the comparison between the computational and experimental determination of electronic circular dichroism spectra of different guanine quadruplexes obtained from human telomeric sequences. In particular the difference between parallel, antiparallel, and hybrid structures is evidenced, as well as the induction of transitions between the polymorphs depending on the solution environment. Extensive molecular dynamics simulations (MD) are used to probe the conformational space of the different quadruplexes, and subsequently state-of-the-art hybrid quantum mechanics/molecular mechanics (QM/MM) techniques coupled with excitonic semiempirical Hamiltonian are used to simulate the macromo…

Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes

By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channe…

Structure-Directing and High-Efficiency Photocatalytic Hydrogen Production by Ag Clusters

H2 production by water splitting is hindered mainly by the lack of low-cost and efficient photocatalysts. Here we show that sub-nanometric silver clusters can catalyze the anisotropic growth of gold nanostructures by preferential adsorption at certain crystal planes of Au seeds, with the result that the final nanostructure can be tuned via the cluster/seed ratio. Such semiconducting Ag clusters are extremely stable and retain their electronic structure even after adsorption at the tips of Au nanorods, enabling various photocatalytic experiments, such as oxygen evolution from basic solutions. In the absence of electron scavengers, UV irradiation generates photoelectrons, which are stored wit…

Identification and validation of novel molecules obtained by integrated computational and experimental approaches for the read-through of PTCs in CF cells

Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

ABSTRACTCoronaviruses may produce severe acute respiratory syndrome (SARS). As a matter of fact, a new SARS-type virus, SARS-CoV-2, is responsible of a global pandemic in 2020 with unprecedented sanitary and economic consequences for most countries. In the present contribution we study, by all-atom equilibrium and enhanced sampling molecular dynamics simulations, the interaction between the SARS Unique Domain and RNA guanine quadruplexes, a process involved in eluding the defensive response of the host thus favoring viral infection of human cells. Our results evidence two stable binding modes involving an interaction site spanning either the protein dimer interface or only one monomer. The …

Does Ligand Symmetry Play a Role in the Stabilization of DNA G-Quadruplex Host-Guest Complexes?

In efforts to find agents with improved biological activity against cancer cells, recent years have seen an increased interest in the study of small molecules able to bind the deoxyribonucleic acid (DNA) when it assumes secondary structures known as G-quadruplexes (G4s) preferring them over the B form. Currently, several compounds reported in literature have already shown to be good candidates as G4s DNA stabilizers. Even though some specific features for the G4s affinity are known, such as a π-delocalized system able to stack at the top/end of a G-tetrad and positively charged substituents able to interact with the grooves, it is not clear yet what kind of structural features affect more t…

Exploring the Chemoselectivity towards Cysteine Arylation by Cyclometallated Au III Compounds: New Mechanistic Insights

To gain more insight into the factors controlling the efficient cysteine arylation by cyclometalated Au(III) complexes, the reaction between selected gold compounds and different peptides was investigated by high‐resolution liquid chromatography electrospray ionization mass spectrometry (HR‐LC‐ESI‐MS). The deducted mechanisms of C–S cross‐coupling, also supported by density functional theory (DFT) and quantum mechanics/molecular mechanics (QM/MM) calculations, evidenced the key role of secondary peptidic gold binding sites in favouring the process of reductive elimination.

Confinement effects on the interactions of native DNA with Cu(II)-5-triethyl ammonium methyl salicylidene orto-phenylendiiminate in C12E4 liquid crystals

Confinement effects of native calf thymus DNA interacting with the complex Cu(ii)-5-(triethylammoniummethyl)salicylidene ortho-phenylendiiminate (CuL(2+)) perchlorate in tetraethylene glycol monododecyl ether (C(12)E(4)) liquid crystals have been investigated by UV absorption spectrophotometry, circular dichroism (CD) and small angle X-ray scattering (SAXS). The results indicate the occurrence of dramatic structural changes of both the DNA and the CuL(2+)-DNA system, when going from aqueous solution to C(12)E(4) liquid crystals, due to confinement constrains imposed by the closed structure of C(12)E(4) reverse micelles. Further marked departures from the behaviour observed in aqueous soluti…

Metal complex-DNA binding: Insights from molecular dynamics and DFT/MM calculations.

Molecular dynamics (MD) simulations, followed by density functional theory/molecular mechanics (DFT/MM) calculations, provided a detailed structure of the binding site between the cationic metallointercalator (dipyrido [3,2-a:2',3'-c]phenazine)(glycinato)copper(II), [Cu(gly)(dppz)](+), and the two dodeca-deoxynucleotide duplexes [dodeca(dG-dC)]2 and [dodeca(dA-dT)]2. Three simultaneous DNA binding types were detected in the fully optimized DFT/MM structures: 1) metal coordination through exocyclic oxygen atoms of nitrogen bases; 2) intercalation of the dppz chromophore between stacked Watson-Crick AT-AT and GC-GC bases; and 3) hydrogen bonding between the glycinato ligand and amine groups o…

X‐ray Absorption Spectra of Cu II and Cu III Complexes of N , N ′ ‐1,2‐Phenylenebis(2‐mercapto‐2‐methylpropionamide)

The X-ray absorption spectra of Cu I I and Cult complexes of N,N'-1,2-phenylenebis(2-mercapto-2-methylpropionamide) were recorded and analysed in solid phase. The EXAFS spectra of the two samples were refined with full multiple scattering path. Geometry optimisations on the Cu I I and Cu I I I complexes were performed by the B3LYP density functional method, with the 6-31G(d,p) basis set, considering different spin multiplicities. The singlet state of the Cu I I I complex was shown to be more stable than the triplet state, and a good agreement between the calculated and the corresponding experimental structure was found. Further single-point calculations on the optimised geometry were carrie…

Analytic high-order Douglas-Kroll_Hess electric field gradients

2-methoxyestradiol impacts on amino acids-mediated metabolic reprogramming in osteosarcoma cells by interaction with NMDA receptor

Deregulation of serine and glycine metabolism, have been identified to function as metabolic regulators in supporting tumor cell growth. The role of serine and glycine in regulation of cancer cell proliferation is complicated, dependent on concentrations of amino acids and tissue-specific. D-serine and glycine are coagonists of N-methyl-D-aspartate receptor subunit GRIN1. Importantly, NMDA receptors are widely expressed in cancer cells and play an important role in regulation of cell death, proliferation and metabolism of numerous malignancies. The aim of the present work was to associate the metabolism of glycine and D-serine with the anticancer activity of 2-methoxyestradiol. 2-methoxyest…

The mechanism of aquaporin inhibition by gold compounds elucidated by biophysical and computational methods

The inhibition of water and glycerol permeation via human aquaglyceroporin-3 (AQP3) by gold(iii) complexes has been studied by stopped-flow spectroscopy and, for the first time, its mechanism has been described using molecular dynamics (MD), combined with density functional theory (DFT) and electrochemical studies. The obtained MD results showed that the most effective gold-based inhibitor, anchored to Cys40 in AQP3, is able to induce shrinkage of pores preventing glycerol and water permeation. Moreover, the good correlation between the affinity of the Au(iii) complex to Cys binding and AQP3 inhibition effects was highlighted, while no influence of the different oxidative character of the c…

DNA interaction of CuII, NiII and ZnII functionalized salphen complexes: studies by linear dichroism, gel electrophoresis and PCR.

The interaction of salphen-type NiII, CuII and ZnII complexes with native DNA was investigated by exploiting linear dichroism experiments. The NiII complex behaves as a typical intercalator, binding strongly and stiffening and unwinding the DNA. The strength of the DNA interaction is slightly weaker for the copper complex and much weaker for the zinc complex. Plasmid-DNA gel electrophoresis experiments indicated that while CuII and ZnII complexes do not induce the unwinding of supercoiled DNA, the NiII complex has a nuclease activity without the addition of external agents. On the other hand, as shown in the PCR assays, we demonstrate that, at the used concentrations, only the CuII complex …

DFT computational study on Fe(III)-N,N′-ethylene-bis(salicylideneiminato) derivatives

DFT calculations, at unrestricted B3LYP level, have been performed on the structures of three iron(III) complexes, Fe(Salen)Cl, [Fe(Salen)]+ and [Fe(Salen)OH2]+, where Salen is the anion of Schiff base ligand N,N′-ethylene-bis (salicylideneimine), considering the spin multiplicity (S) values 2, 4 and 6. The results obtained have been compared with the available structural an magnetic experimental data, allowing us to conclude that a stable form of the FeIII(Salen) complex in aqueous solution should be characterized by an energy stabilization of the S=4 compared to the S=6 state.

Carbon–Phosphorus Coupling from C^N Cyclometalated Au III Complexes

Abstract With the aim of exploiting new organometallic species for cross‐coupling reactions, we report here on the AuIII‐mediated Caryl−P bond formation occurring upon reaction of C^N cyclometalated AuIII complexes with phosphines. The [Au(C^N)Cl2] complex 1 featuring the bidentate 2‐benzoylpyridine (CCON) scaffold was found to react with PTA (1,3,5‐triaza‐7‐phosphaadamantane) under mild conditions, including in water, to afford the corresponding phosphonium 5 through C−P reductive elimination. A mechanism is proposed for the title reaction based on in situ 31P{1H} NMR and HR‐ESI‐MS analyses combined with DFT calculations. The C−P coupling has been generalized to other C^N cyclometalated Au…

Green Tea Catechins Induce Inhibition of PTP1B Phosphatase in Breast Cancer Cells with Potent Anti-Cancer Properties: In Vitro Assay, Molecular Docking, and Dynamics Studies

The catechins derived from green tea possess antioxidant activity and may have a potentially anticancer effect. PTP1B is tyrosine phosphatase that is oxidative stress regulated and is involved with prooncogenic pathways leading to the formation of a.o. breast cancer. Here, we present the effect of selected green tea catechins on enzymatic activity of PTP1B phosphatase and viability of MCF-7 breast cancer cells. We showed also the computational analysis of the most effective catechin binding with a PTP1B molecule. We observed that epigallocatechin, epigallocatechin gallate, epicatechin, and epicatechin gallate may decrease enzymatic activity of PTP1B phosphatase and viability of MCF-7 cells.…

Role of Seroalbumin in the Cytotoxicity of cis-Dichloro Pt(II) Complexes with (N^N)-Donor Ligands Bearing Functionalized Tails

Given the potent anticancer properties of cisdiamminedichloroplatinum( II) and knowing its mode of action, we synthesized four new cis-[PtCl2(N^N)] organoplatinum complexes, two with N-substituted pbi ligands (pbiR = 1-R-2-(2-pyridyl)benzimidazole) (namely, 1 and 2) and two more with 4,4′-disubstituted bpy ligands (bpy = 2,2′-bipyridine) (namely, 3 and 4). We explored their cytotoxicity and ability to bind to deoxyguanosine monophosphate (dGMP), DNA, and albumin models. By 1H NMR and UV−vis spectroscopies, circular dichroism, agarose gel electrophoresis, differential scanning calorimetry measurements, and density functional theory calculations, we verified that only 3 can form aquacomplex s…

The interaction of native DNA with iron(III)- N ,N'-ethylene-bis(salicylideneiminato)-chloride.

Abstract The interaction between native calf thymus deoxyribonucleic acid (DNA) and Fe III - N , N ′ -ethylene-bis (salicylideneiminato)-chloride, Fe(Salen)Cl, was investigated in aqueous solutions by UV–visible (UV–vis) absorption, circular dichroism (CD), thermal denaturation and viscosity measurements. The results obtained from CD, UV–vis and viscosity measurements exclude DNA intercalation and can be interpreted in terms of an electrostatic binding between the Fe(Salen) + cation and the phosphate groups of DNA. The trend of the UV–vis absorption band of the Fe(Salen)Cl complex at different ratios [DNA phosphate ]/[Fe(Salen)Cl] and the large increase of the melting temperature of DNA in …

1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, through 1,3-Dipolar Cycloadditions

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…

Thermodynamics of the interaction between the spike protein of severe acute respiratory syndrome- coronavirus-2 and the receptor of human angiotensin converting enzyme 2. Effects of possible ligands

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 180,000 deaths all over the world, still lacking a medical treatment despite the concerns of the whole scientific community. Human Angiotensin-Converting Enzyme 2 (ACE2) was recently recognized as the transmembrane protein serving as SARS-CoV-2 entry point into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the complex and of the effects of possible ligands. Moreover, binding free energy between ACE2 and the active Receptor Binding Domain (RB…

Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives.

Abstract Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importanc…

Systematic conformational search analysis of the SRR and RRR epimers of 7-hydroxymatairesinol

An extensive and systematic conformational search was performed on the two epimers of the natural lignan 7-hydroxymatairesinol (HMR), by means of a home-made Systematic Conformational Search Analysis (SCSA) code, designed to select more and more stable conformers through sequential geometry optimization of trial structures at increasing levels of calculation theory. In the present case, the starting molecular structures were selected by the semi-empirical AM1 method and filtered – i.e. decreased in number by choosing the more stable species – on the basis of their energy calculated by the HF method and the 6-31G(d) basis set. The geometries obtained were further refined by performing densit…

Novel atrazine-binding biomimetics inspired to the D1 protein from the photosystem II of Chlamydomonas reinhardtii.

Biomimetic design represents an emerging field for improving knowledge of natural molecules, as well as to project novel artificial tools with specific functions for biosensing. Effective strategies have been exploited to design artificial bioreceptors, taking inspiration from complex supramolecular assemblies. Among them, size-minimization strategy sounds promising to provide bioreceptors with tuned sensitivity, stability, and selectivity, through the ad hoc manipulation of chemical species at the molecular scale. Herein, a novel biomimetic peptide enabling herbicide binding was designed bioinspired to the D1 protein of the Photosystem II of the green alga Chlamydomonas reinhardtii. The D1…

Are compliance constants ill-defined descriptors for weak interactions?

Just as the potential energy can be written as a quadratic form in internal coordinates, so it can also be expanded in terms of generalized forces. The resulting coefficients are termed compliance constants. In this article, the suitability of compliance constants as non-covalent bond strength descriptors is studied (a) for a series of weakly bound hydrogen halide–rare gas complexes applying a configuration interaction theory, (b) for a double stranded DNA 4-mer using approximate density functional methods and finally (c) for a double stranded DNA 20-mer using empirical force fields. Our results challenge earlier studies, which concluded the inappropriateness of compliance constants as soft…

Synthesis, characterization and DNA binding studies of potential G4 stabilizer metal complexes

Relativistic coupled cluster calculations of the electronic structure of KrH+, XeH+ and RnH+

Potential energy curves of NgH+ cations (Ng = Kr, Xe, Rn) were obtained by using four-component relativistic CCSD(T) coupled cluster calculations. Dissociation energies, equilibrium bond lengths, electronic properties, such as dipole moments and electric field gradients at the nuclei, and the related spectroscopic parameters of the electronic ground state have been determined. The results obtained for KrH+ and XeH+ are in good agreement with available experimental data, while those for RnH+ have been determined for the first time at this level of theory.

Semiempirical calculations on the interaction between dimethyltin(IV) and DNA model system

Abstract The interaction between a dinucleotide triphosphate duplex (DD), mimicking the DNA molecule, and the dimethyltin(IV) cation is studied by the semiempirical PM3 method. The results show that the interaction can occur involving the tin atom and the electron-donor centres of DD, requiring in some cases the presence of water molecules. In particular, the binding of the dimethyltin(IV) moiety with two adjacent phosphate oxygen atoms is allowed by the presence of water molecules coordinating to the tin atom. In this case the tin environment shows a geometry in agreement with 119 Sn Mossbauer and X-ray data.

Hydrogenation of light hydrocarbons on palladium: theoretical study of the local surface arrangements

Abstract Quantum mechanical calculations at HF, MP2 and DFT levels were used to rationalise the surface effects of the hydrocarbon lateral interactions occurring on single planar metal surfaces or on different adjacent surfaces during the hydrogenation on palladium catalyst. The different values of electronic charge, found in the different atoms of palladium clusters, were suggested as a possible explanation of the non-homogeneous behaviour already inferred for catalyst surface sites having non-isotropic local arrangement.

Novel Sortase A Inhibitors to Counteract Gram-Positive Bacterial Biofilms

Sortase A (SrtA) is a membrane enzyme responsible for the covalent anchoring of surface proteins on the cell wall of Gram-positive bacteria. Nowadays it is considered an interesting target for the development of new anti-infective drugs which aim to interfere with important Gram-positive virulence mechanisms. Along the years, we studied the anti-staphylococcal and anti-biofilm activity of some natural and synthetic polyhalogenated pyrrolic compounds, called pyrrolomycins. Some of them were active on Gram-positive pathogens at a μg/mL range of concentration (1.5-0.045 μg/mL) and showed a biofilm inhibition in the range of 50-80%. [1-3] In light of these encouraging results, herein we present…

Targeting G-quadruplexes with Organic Dyes: Chelerythrine–DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy

The DNA-binding of the natural benzophenanthridine alkaloid chelerythrine (CHE) has been assessed by combining molecular modeling and optical absorption spectroscopy. Specifically, both double-helical (B-DNA) and G-quadruplex sequences&mdash

Computational study of the interaction of proflavine with d(ATATATATAT)2 and d(GCGCGCGCGC)2

Abstract The interaction of proflavine (PR) with two B-DNA decamers of alternating AT and GC sequence, called [deca(dG-dC)]2 and [deca(dA-dT)]2, respectively, was computationally investigated by the ONIOM method, exploiting a three-layer QM/QM/MM hybrid approach. The highest level QM method was applied to the model system, which comprises the intercalation site (5th and 6th base pairs) and the inserted PR molecule. The connecting sugar phosphate backbone was added in the medium layer region. Both higher and medium level layers, differing in the size of the basis set used, were treated by the DFT MPWB1K functional. The full system in the lower layer was described by the empirical AMBER force…

Dissolution of nitrones in alkylphosphates: A structural study

Nitrones are chemical compounds with well-established anti-oxidant and spin-trapping properties. Their low solubility in water for many of them limits their applications, so opportune solvents must be found. In this study, two recently synthetized oxindole nitrones with proven antiproliferative and antioxidant activity have been dissolved in several liquid amphiphiles, chosen as model solvents. The effect of the polar head nature and the alkyl chain length/type have been investigated by a combined experimental (solubility, UV–vis spectroscopy) / computational (molecular dynamics) approach. The different chemical structures of the various solvents offer different chemical environments to the…

Tin-DNA complexes investigated by nuclear inelastic scattering of synchrotron radiation

Nuclear inelastic scattering (NIS) of synchrotron radiation has been used to investigate the dynamics of tin ions chelated by DNA. Theoretical NIS spectra have been simulated with the help of density functional theory (DFT) calculations using 12 models for different binding sites of the tin ion in (CH3)Sn(DNAPhosphate)2. The simulated spectra are compared with the measured spectrum of the tin-DNA complex.

Hydrogen on palladium clusters: a quantum chemical study

Nuclear Quadrupole Moment of 119Sn

Second-order scalar-relativistic Douglas-Kroll-Hess density functional calculations of the electric field gradient, including an analytic correction of the picture change error, were performed for 34 tin compounds of which molecular structures and Sn-119 Mossbauer spectroscopy parameters are experimentally known. The components of the diagonalized electric field gradient tensor, V-xx,V-yy, V-zz, were used to determine the quantity V, which is proportional to the nuclear quadrupole splitting parameter Delta E. The slope of the linear correlation plot of the experimentally determined Delta E parameter versus the corresponding calculated V data allowed us to obtain an absolute value of the nuc…

Molecular-Level Characterization of Heterogeneous Catalytic Systems by Algorithmic Time Dependent Monte Carlo

Monte Carlo algorithms and codes, used to study heterogeneous catalytic systems in the frame of the computational section of the NANOCAT project, are presented along with some exemplifying applications and results. In particular, time dependent Monte Carlo methods supported by high level quantum chemical information employed in the field of heterogeneous catalysis are focused. Technical details of the present algorithmic Monte Carlo development as well as possible evolution aimed at a deeper interrelationship of quantum and stochastic methods are discussed, pointing to two different aspects: the thermal-effect involvement and the three-dimensional catalytic matrix simulation. As topical app…

Catalytic Supported System Modelled by Computational Approaches

Studi spettroscopici su complessi indolotriazolopirimidina-DNA nativo.

IDEA: interface dynamics and energetics algorithm.

IDEA, interface dynamics and energetics algorithm, was implemented, in FORTRAN, under different operating systems to mimic dynamics and energetics of elementary events involved in interfacial processes. The code included a parallel elaboration scheme in which both the stochastic and the deterministic components, involved in the developed physical model, worked simultaneously. IDEA also embodied an optionally running VISUAL subroutine, showing the dynamic energy changes caused by the surface events, e.g., occurring at the gas-solid interface. Monte Carlo and ordinary differential equation system subroutines were employed in a synergistic way to drive the occurrence of the elementary events a…

Structure Validation of Natural Products by Quantum-Mechanical GIAO Calculations of 13C NMR Chemical Shifts GIAO=gauge including atomic orbitals.

Geometry optimization and GIAO (gauge including atomic orbitals) 1 3 C NMR chemical shift calculations at Hartree-Fock level, using the 6-31G(d) basis set, are proposed as a tool to be applied in the structural characterization of new organic compounds, thus providing useful support in the interpretation of experimental NMR data. Parameters related to linear correlation plots of computed versus experimental 1 3 C NMR chemical shifts for fourteen low-polar natural products, containing 10-20 carbon atoms, were employed to assess the reliability of the proposed structures. A comparison with the hybrid B3LYP method was carried out to evaluate electron correlation contributions to the calculatio…

The dissociation of the Hsp60/pro-Caspase-3 complex by bis(pyridyl)oxadiazole copper complex (CubipyOXA) leads to cell death in NCI-H292 cancer cells

Abstract Cell survival and proliferation are central to carcinogenesis, involving various mechanisms among which those that impede apoptosis are important. In this, the role of the molecular chaperone Hsp60 is unclear since it has been reported that it can be both, pro- or anti-apoptotic. A solution to this riddle is crucial to the development of anti-cancer therapies targeting Hsp60. We addressed this question using a tumor cell line, NCI-H292, and [Cu(3,5-bis(2′-pyridyl)-1,2,4-oxadiazole) 2 (H 2 O) 2 ](ClO 4 ) 2 , CubipyOXA , a copper-containing compound with cytotoxic properties. We treated cells with various doses of the compound and measured cell viability; apoptosis indicators; and le…

Chitosan Film Functionalized with Grape Seed Oil—Preliminary Evaluation of Antimicrobial Activity

Although the fishing and wine industries undoubtedly contribute significantly to the economy, they also generate large waste streams with considerable repercussions on both economic and environmental levels. Scientific literature has shown products can be extracted from these streams which have properties of interest to the cosmetics, pharmaceutical and food industries. Antimicrobial activity is undoubtedly among the most interesting of these properties, and particularly useful in the production of food packaging to increase the shelf life of food products. In this study, film for food packaging was produced for the first time using chitosan extracted from the exoskeletons of red shrimp (Ar…

Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions

AbstractHuman telomeric DNA (h-Telo), in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics (MD) simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.

Photochemical Functionalization of Allyl Benzoates by C-H Insertion

The photoreactivity of allyl benzoates, containing an electron-rich double bond, has been explored by irradiation at 305 nm in different solvents. Solvent addition products arising from an insertion of the alpha H–C bonds of THF, dioxane, and i-PrOH to the allylic double bond was realized. The observed reactivity depended on reaction conditions and substitution pattern of the substrate. A DFT study on this unusual reaction was performed allowing the formulation of two mechanistic pathways.

Synthesis and chemical characterization of CuII, NiII and ZnII complexes of 3,5-bis(2′-pyridyl)-1,2,4-oxadiazole and 3-(2′-pyridyl)5-(phenyl)-1,2,4-oxadiazole ligands

Abstract The synthesis and structural characterization of Ni II , Cu II and Zn II complexes of two chelating 1,2,4-oxadiazole ligands, namely 3,5-bis(2′-pyridyl)-1,2,4-oxadiazole (bipyOXA) and 3-(2′-pyridyl)5-(phenyl)-1,2,4-oxadiazole (pyOXA), is here reported. The formed hexacoordinated metal complexes are [M(bipyOXA) 2 (H 2 O) 2 ](ClO 4 ) 2 and [M(pyOXA) 2 (ClO 4 ) 2 ], respectively (M = Ni, Cu, Zn). X-ray crystallography, 1 H and 13 C NMR spectroscopy and C, N, H elemental analysis data concord in attributing them an octahedral coordination geometry. The two coordinated pyOXA ligands assume a trans coplanar disposition, while the two bipyOXA ligands are not. The latter result is a possib…

Pirazolo[3,4-d][1,2,3]triazolo[1,5-a]pirimidina: accesso sintetico tramite cicloaddizioni 1,3-dipolari e riarrangiamento di Dimroth

CO on Nickel: some computational insights about steric hindrance in loaded surfaces

In silico, spectroscopic, and biological insights on annelated pyrrolo[3,2-e]pyrimidines with antiproliferative activity

The in silico COMPARE analysis was performed on 8-[3-(piperidino)propyl]-4,10-dimethyl-9-phenyl-6-(methylsulfanyl)-3,4-dihydropyrimido[1,2-c]pyrrolo[3,2-e]pyrimidin-2(8H)-one, a compound with promising antiproliferative activity, previously synthetized and screened against a panel of 60 human tumor cell lines. The results evidenced that this compound matches the biological properties of Chromomycin A3 and Actinomycin D, known drugs with high DNA binding affinity. Prompted by such results, a thorough spectroscopic investigation of its DNA aqueous solutions was performed, with the aim to verify its DNA-binding properties. DNA groove-binding interaction was assigned by UV-vis spectrophotometri…

A Simple Entropic-Driving Separation Procedure of Low-Size Silver Clusters, Through Interaction with DNA

Abstract Synthesis and purification of metal clusters without strong binding agents by wet chemical methods are very attractive for their potential applications in many research areas. However, especially challenging is the separation of uncharged clusters with only a few number of atoms, which renders the usual techniques very difficult to apply. Herein, we report the first efficient separation of Ag2 and Ag3 clusters using the different entropic driving forces when such clusters interact with DNA, into which Ag3 selectively intercalates. After sequential dialysis of the samples and denaturalizing the DNA‐Ag3 complex, pure Ag2 can be found in the dialysate after extensive dialysis. Free Ag…

The inhibition of glycerol permeation through aquaglyceroporin-3 induced by mercury(II)

Mercurial compounds are known to inhibit water permeation through aquaporins (AQPs). Although in the last years some hypotheses were proposed, the exact mechanism of inhibition is still an open question and even less is known about the inhibition of the glycerol permeation through aquaglyceroporins. Molecular dynamics (MD) simulations of human aquaporin-3 (AQP3) have been performed up to 200 ns in the presence of Hg2+ ions. For the first time, we have observed the unbiased passage of a glycerol molecule from the extracellular to cytosolic side. Moreover, the presence of Hg2+ ions covalently bound to Cys40 leads to a collapse of the aromatic/arginine selectivity filter (ar/R SF), blocking th…

Synthesis, characterization, cellular uptake and interaction with native DNA of a bis(pyridyl)-1,2,4-oxadiazole copper(II) complex

The copper(II) complex of 3,5-bis(2'-pyridyl)-1,2,4-oxadiazole was synthesized and characterized. X-Ray crystallography revealed that the complex consists of a discrete [Cu(3,5-bis(2'-pyridyl)-1,2,4-oxadiazole)(2)(H(2)O)(2)](2+) cation and two ClO(4)(-) anions. The Cu(II) coordination sphere has a distorted octahedral geometry and each ligand chelates the copper ion through the N(4) nitrogen of the oxadiazole ring and the nitrogen of one pyridine moiety. The coordinated water molecules are in cis position and each of them is H-bonded to the 5-pyridyl nitrogen of the oxadiazole ligand and to an oxygen of the perchlorate anion. Biological assays showed that, despite the free ligand not being …

Selective targeting of PARP-1 zinc finger recognition domains with Au(III) organometallics

The binding of Au(iii) complexes to the zinc finger domain of the anticancer drug target PARP-1 was studied using a hyphenated mass spectrometry approach combined with quantum mechanics/molecular mechanics (QM/MM) studies. Competition experiments were carried out, whereby each Au complex was exposed to two types of zinc fingers. Notably, the cyclometallated Au-C^N complex was identified as the most selective candidate to disrupt the PARP-1 zinc finger domain, forming distinct adducts compared to the coordination compound Auphen.

THE INTERACTION OF NATIVE DNA WITH Ni(II), Cu(II) and Zn(II) COMPLEXES OF 5-TRIETHYL AMMONIUM METHYL SALICYLIDENE ORTHO-PHENYLENDIIMINE

Double chained naphthalenes as G4 binders

Combined spectroscopic and theoretical analysis of the binding of a water-soluble perylene diimide to DNA/RNA polynucleotides and G-quadruplexes.

We present here a combined spectroscopic and theoretical analysis of the binding of N,N’-bis(2-(1-piperazino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide dichloride (PZPERY) to different biosubstrates. Absorbance titrations and circular dichroism experiments, melting studies and isothermal calorimetry (ITC) titrations reveal a picture where the binding to natural double-stranded DNA is very different from that to double and triple-stranded RNAs (poly(A)∙poly(U) and poly(U)∙poly(A)⁎poly(U)). As confirmed also by the structural and energetic details clarified by density functional theory (DFT) calculations, intercalation occurs for DNA, with a process driven by the combination of aggr…

Adsorbed CO on group 10 metal fragments: A DFT study

DFT calculations on the helicopter and cartwheel rotations of one CO molecule adsorbed at the bridge site on metal-surface fragments, characterized by two (M(8)) or three (M(14)) metal-atom layers (M = Ni, Pd, Pt) were performed by the B3LYP[LANL2DZ+6-31 g(d,p)] method, to rationalize the adsorption energetics and the steric hindrance characteristics of surface CO molecules. Potential Energy Surfaces were obtained, either fixing the C-O bond-length or allowing it to change. The behavior of the three metals, as obtained from the study of the configurational space characterizing the CO adsorption on the fragments was explained on the basis of the interaction energies involved in the different…

Experimental and theoretical characterization of the strong effects on DNA stability caused by half-sandwich Ru(II) and Ir(III) bearing thiabendazole complexes

Abstract: The synthesis and characterization of two half-sandwich complexes of Ru(II) and Ir(III) with thiabendazole as ancillary ligand and their DNA binding ability were investigated using experimental and computational methods. 1H NMR and acid–base studies have shown that aquo-complexes are the reactive species. Kinetic studies show that both complexes bind covalently to DNA through the metal site and non covalently through the ancillary ligand. Thermal stability studies, viscosity, circular dichroism measurements and quantum chemical calculations have shown that the covalent binding causes breaking of the H-bonding between base pairs, bringing about DNA denaturation and compaction. Addi…

Conformational analysis and DFT calculations of 8α-hydroxy-germacradiene-6,12-olide derivatives

The Systematic Conformational Search Analysis (SCSA) code was employed to study the conformational properties of the 8α-hydroxy-germacradiene-6,12-olide isomers. This procedure was extended to the trans,cis- and trans,trans-1(10),4-isomers of 8α,15-dihydroxy-germacradiene-6,12-olides and 8α-hydroxy-15-oxo-germacradiene-6,12-olides, to investigate structural and energetic analogies between these and the 8α-hydroxy-germacradiene-6,12-olide species. The calculated 13C NMR spectra, at the hybrid DFT mPW1PW91 level, showed a sound correlation with the corresponding experimental spectra, providing a valid support to the reliability of the calculated structures and to the consistence of our confor…

Spectroscopic study of the interaction of Ni(II)-5-triethyl ammonium methyl salicylidene ortho-phenylendiiminate with native DNA.

The interaction of native calf thymus DNA with the cationic Ni(II) complex of 5-triethyl ammonium methyl salicylidene ortho-phenylendiimine (NiL(2+)), in 1mM Tris-HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The dramatic modification of the DNA CD spectrum, the appearance of a broad induced CD band in the range 350-400nm, the strong increase of the DNA melting temperature (T(m)) and the fluorescence quenching of ethidium bromide-DNA solutions, in the presence of increasing amounts of the NiL(2+) metal complex, support the existence of a tig…

A novel copper compound, CuNV110, induces apoptosis in tumor cells by dissociation of the Hsp60- pro-caspase 3 complex

The biological activity of CuNV1110, a novel copper chemical compound, has been recently studied on cancer cells and it has been showed that it reduces the cell viability, in a dose and time dependent manner, and induces cell apoptosis. In this study we evaluated the possible mechanisms by which CuNV1110 induces cell apoptosis. In particular we looked at its effects on Hsp60 levels and caspase 3 activation. We used an in vitro model of a pulmonary mucoepidermoid carcinoma (NCI-H292 cells). We found that CuNV1110 reduces the cell viability and induces cell apoptosis in a dose/time dependent manner. Then, we found that Hsp60 levels decrease with the increasing concentrations of CuNV110; by co…

On the interaction of doxorubicin with polynucleotides

The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (poly-AT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV−vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.

Structural investigations on diorgano- and triorganotin(IV) derivatives of [meso-tetra(4-sulfonatophenyl)porphine]metal chlorides.

Abstract Several new complexes of organotin(IV) moieties with MCln[meso-tetra(4-sulfonatophenyl)porphine], (R2Sn)2MCln[meso-tetra(4-sulfonatophenyl)-porphinate]s and (R3Sn)4MCln [meso-tetra(4-sulfonatophenyl)porphinate]s, [M = Fe(III), Mn(III): n = 1, R = Me, n-Bu; Ph; M = Sn(IV): n = 2, R = Me, n-Bu] have been synthesized and their solid state configuration investigated by infrared (IR) and Mossbauer spectroscopy, and by 1H and 13C NMR in D2O. The electron density on the metal ion coordinated inside the porphyrin ring is not influenced by the organotin(IV) moieties bonded to the oxygen atoms of the side chain sulfonatophenyl groups, as it has been inferred on the basis of Mossbauer spectro…

Catalytic activity of T22 H-ZSM-5 zeolite on the trans–cis 2-butene isomerization

CuNV1110 induces dissociation of the Hsp60-pro-caspase 3 complex and activation of apoptosis in tumor cells

On the structure of 3-acetylamino-5-methyl-1,2,4-oxadiazole and on the fully degenerate rearrangements (FDR) of its anion: a stimulating comparison between the results of ‘in-silicon chemistry’ and ‘laboratory chemistry’

An accurate crystal structure determination has provided evidence for a planar conformation for 3-acetylamino-5-methyl-1,2,4-oxadiazole (5), in agreement with quantum-mechanical calculations in the gas phase. In the crystal, a series of strong intermolecular N7H7….O9 hydrogen bonds link the amido groups of different molecules, causing the formation of infinite parallel ordered chains. The effect of the DMSO solvent on the energy and charge distribution of compound 5 and on its relevant 5− anion, involved in a fully degenerate rearrangement (FDR), has been deepened by quantum-mechanical DFT calculations. The calculated energy barrier for the FDR increases in going from in vacuo to DMSO, in a…

Dynamics of Metal Centers Monitored by Nuclear Inelastic Scattering

Nuclear inelastic scattering of synchrotron radiation has been used now since 10 years as a tool for vibrational spectroscopy. This method has turned out especially useful in case of large molecules that contain a M\"ossbauer active metal center. Recent applications to iron-sulfur proteins, to iron(II) spin crossover complexes and to tin-DNA complexes are discussed. Special emphasis is given to the combination of nuclear inelastic scattering and density functional calculations.

Structure of the 5′ untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune systemviathe human oligoadenylate synthase 1

2′-5′-Oligoadenylate synthetase 1 (OAS1) is one of the key enzymes driving the innate immune system response to SARS-CoV-2 infection whose activity has been related to COVID-19 severity. OAS1 is a sensor of endogenous RNA that triggers the 2′-5′-oligoadenylate/RNase L pathway. Upon SARS-CoV-2 infection, OAS1 is responsible for the recognition of viral RNA and has been shown to possess a particularly high sensitivity for the 5′-untranslated (5′-UTR) RNA region, which is organized in a double-strand stem loop motif (SL1). Here we report the structure of the SL1/OAS1 complex also rationalizing the high affinity for OAS1.

Forever Young: Structural Stability of Telomeric Guanine Quadruplexes in the Presence of Oxidative DNA Lesions**

International audience; Human telomeric DNA, in G-quadruplex (G4) conformation, is characterized by a remarkable structural stability that confers it the capacity to resist to oxidative stress producing one or even clustered 8-oxoguanine (8oxoG) lesions. We present a combined experimental/computational investigation, by using circular dichroism in aqueous solutions, cellular immunofluorescence assays and molecular dynamics simulations, that identifies the crucial role of the stability of G4s to oxidative lesions, related also to their biological role as inhibitors of telomerase, an enzyme overexpressed in most cancers associated to oxidative stress.

Conformational analysis and DFT calculations of 8 alpha-hydroxy-germacradiene-6,12-olide derivatives

DFT calculations of the electric field gradient of tin compounds: a structure elucidation tool by 119Sn Mossbauer spectroscopy.

Perturbation of Developmental Regulatory Gene Expression by a G-Quadruplex DNA Inducer in the Sea Urchin Embryo.

The G-quadruplex (G4) is a four-stranded DNA structure identified in vivo in guanine-rich regions located in the promoter of a number of genes. Intriguing evidence suggested that small molecules acting as G4-targeting ligands could potentially regulate multiple cellular processes via either stabilizing or disruptive effects on G4 motifs. Research in this field aims to prove the direct role of G4 ligands and/or structures on a specific biological process in a complex living organism. In this study, we evaluate in vivo the effects of a nickel(II)-salnaphen-like complex, named Nisaln, a potent G4 binder and stabilizer, during embryogenesis of the sea urchin embryo. We describe developmental de…

G4-DNA vs. B-DNA binding of Schiff base transition metal complexes

The competitive binding of nickel(II), copper(II) and zinc(II) complexes toward B- and G4-DNA was addressed through spectroscopic titrations and rationalized by computational investigations, consisting of molecular dynamics simulations followed by density functional theory/molecular mechanics (DFT/MM) calculations [1]. The experimental DNA binding studies clearly highlight the selectivity of the compounds, in particular the nickel(II) complex, toward G4-DNA from both h-Telo and c-myc. Moreover, the compounds show biological activity against HeLa and MCF-7 cancer cell lines. Remarkably, the experimental DNA-binding affinity trend of the three metal complexes, obtained from the DNA-binding co…

ChemInform Abstract: Photochemical Functionalization of Allyl Benzoates by C-H Insertion.

The photoreactivity of allyl benzoates, containing an electron-rich double bond, has been explored by irradiation at 305 nm in different solvents. Solvent addition products arising from an insertion of the alpha H–C bonds of THF, dioxane, and i-PrOH to the allylic double bond was realized. The observed reactivity depended on reaction conditions and substitution pattern of the substrate. A DFT study on this unusual reaction was performed allowing the formulation of two mechanistic pathways.

New benzothieno[3,2-d]-1,2,3-triazines with antiproliferative activity: synthesis, spectroscopic studies, and biological activity.

New benzothieno[3,2-d]-1,2,3-triazines, together with precursors triazenylbenzo[b]thiophenes, were designed, synthesized and screened as anticancer agents. The structural features of these compounds prompted us to investigate their DNA binding capability through UV–vis absorption titrations, circular dichroism, and viscometry, pointing out the occurrence of groove-binding. The derivative 3-(4-methoxy-phenyl)benzothieno[3,2-d]-1,2,3-triazin-4(3H)-one showed the highest antiproliferative effect against HeLa cells and was also tested in cell cycle perturbation experiments. The obtained results assessed for the first time the anticancer activity of benzothieno[3,2-d]-1,2,3-triazine nucleus, and…

Complessi di Platinum(II): sintesi, studi di DNA-binding e loro attività antitumorale in vitro

Con lo scopo di trovare nuovi analoghi del Cis-DDP (cis-diammino dicloro platino(II)) nuovi complessi del platino sono stati sintetizzati, caratterizzati e ne è stata studiata l’attività antitumorale in vitro [1]. Recentemente sono stati preparati complessi con metalli del quarto periodo di transizione con entrambi i leganti, dipirido[3,2-a:2’,3’-c]fenazina (dppz) e glicinato (gly) [2]. I composti di nuova sintesi vengono generalmente caratterizzati attraverso parecchie tecniche analitiche incluso la cristallografia a raggi-X e la loro attività antitumorale viene testata su un vasto pannello di linee cellulari umane [1,2]. Le proprietà biologiche spesso sono correlate alla loro interazione …

The interaction of DNA with metal complexes: experimental and computational studies

Progettazione e sintesi di nuovi complessi metallici potenziali inibitori di FGFR4

I pathways di segnalazione che coinvolgono il recettore del fattore di crescita dei fibroblasti 4 (FGFR4) risultano alterati in varie tipologie di tumori [1] ed è stato dimostrato come l’interruzione della segnalazione FGF19/FGFR4 interrompa la proliferazione e induca l’apoptosi delle cellule tumorali, offrendo grandi promesse terapeutiche. [2-4] Allo scopo d’individuare nuovi leganti FGFR4, sono stati effettuati degli studi di modellistica molecolare (Fig. 1) che, riferendosi alla struttura del ponatinib, noto inibitore di FGFR4, [5] il cui utilizzo è ostacolato dall’elevata lipofilia e da effetti secondari, hanno consentito di generare una “Drug Discovery Library” di oltre 30 nuovi potenz…

Silver Atomic Quantum Clusters of Three Atoms for Cancer Therapy: Targeting Chromatin Compaction to Increase the Therapeutic Index of Chemotherapy

Nanomaterials with very low atomicity deserve consideration as potential pharmacological agents owing to their very small size and to their properties that can be precisely tuned with minor modifications to their size. Here, it is shown that silver clusters of three atoms (Ag3 -AQCs)-developed by an ad hoc method-augment chromatin accessibility. This effect only occurs during DNA replication. Coadministration of Ag3 -AQCs increases the cytotoxic effect of DNA-acting drugs on human lung carcinoma cells. In mice with orthotopic lung tumors, the coadministration of Ag3 -AQCs increases the amount of cisplatin (CDDP) bound to the tumor DNA by fivefold without modifying CDDP levels in normal tiss…

Ag5 nanoclusters with dual catalytic antiradical activities

Silver nanoclusters of five atoms (Ag5) display outstanding catalytic activities for the deactivation of radicals. Using 2,2-diphenyl-1‑picrylhydrazyl (DPPH) radical as a model system, we observed a fast radical reduction to DPPH anions using only [Ag5] 3 to 4 orders of magnitude less than [DPPH]. Moreover, nanoclusters remain stable at the end of the reaction, and can deactivate again DPPH radicals at the same rate, indicating that they act as anti-radical catalysts. The radical scavenger catalytic activity of Ag5 proceeds selectively through the oxidation of methanol (used to dissolve the radical) to formaldehyde, which is supported by DFT calculations. The obtained catalytic rate constan…

PTP1B phosphatase as a novel target of oleuropein activity in MCF-7 breast cancer model.

Phosphatase PTP1B has become a therapeutic target for the treatment of type 2-diabetes, whereas recent studies have revealed that PTP1B plays a pivotal role in pathophysiology and development of breast cancer. Oleuropein is a natural, phenolic compound with anticancer activity. The aim of this study was to address the question whether PTP1B constitutes a target for oleuropein in breast cancer MCF-7 cells. The cellular MCF-7 breast cancer model was used in the study. The experiments were performed using cellular viability tests, Elisa assays, immunoprecipitation, flow cytometry analyses and computer modelling. Herein, we evidenced that the reduced activity of phosphatase PTP1B after treatmen…

SELECTIVE G-QUADRUPLEX STABILIZERS: SALPHEN-LIKE COMPLEXES WITH ANTIPROLIFERATIVE ACTIVITY

Schiff base complexes derived from N,N!-bridged tetradentate ligands involving N2O2 donor atoms present very favourable features to act as G4 binders. Thus, a series of square-planar and square pyramidal metal complexes, ML2+ (M = Ni, Cu, and Zn), have been synthesized and characterized.

Theoretical evaluation of structures and energetics involved in the hydrogenation of hydrocarbons on palladium surfaces

Abstract Quantum mechanical calculations were employed to deepen information about the basic properties of the mechanism occurring in the palladium catalytic hydrogenation involving surface hydrogen species of unsaturated hydrocarbons. Activation energy values of elementary events implicated in the whole reaction were computed by potential energy surface analyses, to determine the corresponding occurrence probabilities of the same events. Different surface hydrogen species were pointed out and their relevance in the overall surface process was discussed together with their geometrical and chemical characteristics.

Determination of the Relative Stereochemistry of Flexible Organic Compounds by Ab Initio Methods: Conformational Analysis and Boltzmann-Averaged GIAO 13C NMR Chemical Shifts GIAO=gauge including atomic orbitals.

Ab initio calculations at the Hartree-Fock level with full-geometry optimization using the 6-31G(d) basis set, and GIAO (gauge including atomic orbitals) 1 3 C NMR chemical shifts, are presented here as a support in the study of the stereochemistry of low-polar organic compounds having an openchain structure. Four linear stereoisomers, fragments of a natural product previously characterized by experimental 1 3 C NMR spectra, which possesses three stereogenic centers, 11 carbon atoms, and 38 atoms in total, were considered. Conformational searches, by empirical force-field molecular dynamics, pointed out the existence of 8-13 relevant conformers per stereoisomer. Thermochemical calculations …

Computational Study of the Hydrogenolysis of Hydroxymatairesinol to Matairesinol

B‐DNA structure and stability: the role of nucleotide composition and order

Abstract We have quantum chemically analyzed the influence of nucleotide composition and sequence (that is, order) on the stability of double‐stranded B‐DNA triplets in aqueous solution. To this end, we have investigated the structure and bonding of all 32 possible DNA duplexes with Watson–Crick base pairing, using dispersion‐corrected DFT at the BLYP‐D3(BJ)/TZ2P level and COSMO for simulating aqueous solvation. We find enhanced stabilities for duplexes possessing a higher GC base pair content. Our activation strain analyses unexpectedly identify the loss of stacking interactions within individual strands as a destabilizing factor in the duplex formation, in addition to the better‐known eff…

The interaction of native calf thymus DNA with Fe(III)- dipyrido[3,2-a:2’,3’-c]phenazine chloride

Molecular recognition of naphthalene diimide ligands by telomeric quadruplex-DNA: the importance of the protonation state and mediated hydrogen bonds.

In depth Monte Carlo conformational scans in combination with molecular dynamics (MD) simulations and electronic structure calculations were applied in order to study the molecular recognition process between tetrasubstituted naphthalene diimide (ND) guests and G-quadruplex (G4) DNA receptors. ND guests are a promising class of telomere stabilizers due to which they are used in novel anticancer therapeutics. Though several ND guests have been studied experimentally in the past, the protonation state under physiological conditions is still unclear. Based on chemical intuition, in the case of N-methyl-piperazine substitution, different protonation states are possible and might play a crucial …

Hsp60, a Novel Target for Antitumor Therapy: Structure-Function Features and Prospective Drugs Design

Heat shock protein 60 kDa (Hsp60) is a chaperone classically believed to be involved in assisting the correct folding of other mitochondrial proteins. Hsp60 also plays a role in cytoprotection against cell stressors, displaying for example, antiapoptotic potential. Despite the plethora of studies devoted to the mechanism of Hsp60's function, especially in prokaryotes, fundamental issues still remain unexplored, including the definition of its role in cancer. Key questions still unanswered pertain to the differences in structure-function features that might exist between the well-studied prokaryotic GroEL and the largely unexplored eukaryotic Hsp60 proteins. In this article we discuss these …

Hydrogenolysis of hydroxymatairesinol on Y derived catalysts: a computational study

Hydrogenolysis of 7-hydroxymatairesinol (HMR) to matairesinol (MAT) occurs on palladium supported acidic catalysts. HMR has three stereochemical centres and naturally exists as a mixture of two diastereoisomers, namely RRR-HMR and SRR-HMR. The latter is significantly more reactive than the former, in the reaction above. In order to elucidate the hydrogenolysis mechanism, simple surface events involving HMR derivatives on aluminated faujasite (H-Y) fragments were simulated by quantum chemical calculations. The metallic function of a Pd/H-Y acidic catalyst was also mimicked by a minimal palladium cluster. Stereochemical evidences pointed already out that water β-elimination on the epimeric ce…

Synthesis of copper(II) complexes of new carbon-scorpionate ligands

A set of new “carbon-based” scorpionate ligands based on S- and N-containing heterocyclic moieties have been synthesized. They offer the advantage of a higher stability with respect to the “classical” boron-based scorpionate ligands and also a certain degree of hydrophilicity. The synthesis of these ligands was accomplished by the coupling reaction of the N-methylimidazolyllithium with a suitable electrophilic partner. The reaction yield ranges from 40% to 65%. Preliminary results on the synthesis and characterization of the related copper(II) complex are also presented.

DNA-Binding and Anticancer Activity of Pyrene-Imidazolium Derivatives

DNA-binding investigations showed that two different derivatives endowed with pyrene and imidazolium moieties, 1 and 2, strongly bind both double-stranded DNA and telomeric sequences in G-quadruplex (G4) conformation. The values of the DNA-binding constants indicate that 1 and 2 show preferential affinity for G4-DNA, of about one and two orders of magnitude, respectively. Moreover, 1 and 2 inhibit short and long-term proliferation of breast cancer cell lines in a time- and dose-dependent fashion. Remarkably, senescence assays indicate that telomeric G4-DNA is a possible biotarget for the cytotoxic activity of 2. Molecular dynamics simulations suggest that the stronger binding of 2 with G4-D…

X-ray absorption spectra of Cu(II)- and Cu(III)- complexes of N,N’-1,2-phenylenebis(2-mercapto-2-methyl-propionamide)

Identification and validation of novel molecules obtained by integrated computational and experimental approaches for the readthrough of PTCs in CF cells

Cystic Fibrosis patients with nonsense-mutation in h-CFTR gene generally make virtually no CFTR protein and thus often have a more severe form of CF. Ataluren (PTC124) was suggested to induce read-through of premature but not normal termination codons. Despite the promising results there is not a general consensus on the mechanism of its action (protein stabilization or codon read-through) and its efficacy, the identification of new PTC124 analogues and the study of the mechanism of action may led to a new strategy for the development of a pharmacologic approach to the cure of CF.

The interaction of native calf thymus DNA with dipyrido[3,2-a;2',3'-c]phenazine and its heteroleptic Iron(III) complexes

Propan-2-ol dehydration on acidic zeolite fragments: a DFT study

Systematic conformational search analysis of the SRR and RRR epimers of 7-hydroxymatairesinol

An extensive and systematic conformational search was performed on the two epimers of the natural lignan 7-hydroxymatairesinol (HMR), by means of a home-made Systematic Conformational Search Analysis (SCSA) code, designed to select more and more stable conformers through sequential geometry optimization of trial structures at increasing levels of calculation theory. In the present case, the starting molecular structures were selected by the semi-empirical AM1 method and filtered – i.e. decreased in number by choosing the more stable species – on the basis of their energy calculated by the HF method and the 6-31G(d) basis set. The geometries obtained were further refined by performing densit…

Design and synthesis of high affinity compounds for the Hsp60 expression control in carcinogenic processes

First observed in cells exposed to high temperatures, Heat shock proteins (Hsps) are nowadays considered the most important cell “chaperone” complexes over-­expressed in response to a number of cell stress stimuli.1 The chaperone activity is the main function of the eukaryotic Heat shock protein 60 kDa (Hsp60), involved in the capture and refold of unfolded or misfolded proteins. Additional roles in signal transduction,2 senescence activation3 and apoptosis4 have been ascribed to cytosolic Hsp60. During the carcinogenIc process, in vivo studies demonstrated increased levels of human Hsp60 in several organs, such as uterine exocervix,5 large bowel,6 and prostate.6 In this context, our study …

Muscle Histopathological Abnormalities in a Patient With a CCT5 Mutation Predicted to Affect the Apical Domain of the Chaperonin Subunit.

Recognition of diseases associated with mutations of the chaperone system genes, e.g., chaperonopathies, is on the rise. Hereditary and clinical aspects are established, but the impact of the mutation on the chaperone molecule and the mechanisms underpinning the tissue abnormalities are not. Here, histological features of skeletal muscle from a patient with a severe, early onset, distal motor neuropathy, carrying a mutation on the CCT5 subunit (MUT) were examined in comparison with normal muscle (CTR). The MUT muscle was considerably modified; atrophy of fibers and disruption of the tissue architecture were prominent, with many fibers in apoptosis. CCT5 was diversely present in the sarcolem…

Deposition of tin sulfide thin films from tin(iv) thiolate precursors

AACVD (aerosol-assisted chemical vapour deposition) using (PhS)(4)Sn as precursor leads to the deposition of Sn3O4 in the absence of H2S and tin sulfides when H2S is used as co-reactant. At 450 degreesC the film deposited consists of mainly SnS2 while at 500 degreesC SnS is the dominant component. The mechanism of decomposition of (PhS)(4)Sn is discussed and the structure of the precursor presented.

Another step toward DNA selective targeting: NiII and CuII complexes of a Schiff base ligand able to bind gene promoter G-quadruplexes

DNA G-rich sequences are able to form four-stranded structures organized in stacked guanine tetrads. These structures, called G-quadruplexes, were found to have an important role in the regulation of oncogenes expression and became, for such a reason, appealing targets for anticancer drugs. Aiming at finding selective G-quadruplex binders, we have designed, synthesized and characterized a new water soluble Salen-like Schiff base ligand and its NiII and CuII metal complexes. UV-Vis, circular dichroism and FRET measurements indicated that the nickel complex can stabilize oncogene promoter G-quadruplexes with high selectivity, presenting no interactions with duplex DNA at all. The same compoun…

A Novel Peptide with Antifungal Activity from Red Swamp Crayfish Procambarus clarkii

The defense system of freshwater crayfish Procambarus clarkii as a diversified source of bioactive molecules with antimicrobial properties was studied. Antimicrobial activity of two polypeptide-enriched extracts obtained from hemocytes and hemolymph of P. clarkii were assessed against Gram positive (Staphylococcus aureus, Enterococcus faecalis) and Gram negative (Pseudomonas aeruginosa, Escherichia coli) bacteria and toward the yeast Candida albicans. The two peptide fractions showed interesting MIC values (ranging from 11 to 700 μg/mL) against all tested pathogens. Polypeptide-enriched extracts were further investigated using a high-resolution mass spectrometry and database search and 14 n…

Ag2 and Ag3 clusters: synthesis, characterization, and interaction with DNA.

Subnanometric samples, containing exclusively Ag2 and Ag3 clusters, were synthesized for the first time by kinetic control using an electrochemical technique without the use of surfactants or capping agents. By combination of thermodynamic and kinetic measurements and theoretical calculations, we show herein that Ag3 clusters interact with DNA through intercalation, inducing significant structural distortion to the DNA. The lifetime of Ag3 clusters in the intercalated position is two to three orders of magnitude longer than for classical organic intercalators, such as ethidium bromide or proflavine. Fil: Buceta, David. Universidad de Santiago de Compostela; España Fil: Busto, Natalia. Unive…

Fluorescence emission and enhanced photochemical stability of Zn(II)-5-triethyl ammonium methyl salicylidene ortho-phenylendiiminate interacting with native DNA.

Abstract The photophysical and photochemical properties of the cationic Zn II complex of 5-triethyl ammonium methyl salicylidene ortho-phenylendiimine (ZnL 2+ ) interacting with native DNA were investigated by steady state and time-resolved fluorescence spectroscopies. Experimental results indicate that, in the presence of DNA, ZnL 2+ is efficiently protected from a photochemical process, which occurs when it is in the free state dispersed in aqueous solution. The analysis of the absorption and emission spectra of ZnL 2+ , both stored in the dark and after exposure to tungsten lamp light for 24 h, corroborated by quantum chemical calculations, allowed us to point out that ZnL 2+ undergoes a…

Fishing for G-quadruplexes in solution with a perylene diimide derivative labeled with biotins

A new fluorescent, non‐cytotoxic perylene diimide derivative with two biotins at the peri position, PDI2B, has been synthesized. This molecule is able to interact selectively with G‐quadruplexes with scarce or no affinity towards single‐ or double‐stranded DNA. These features have made it possible to design a simple, effective, safe, cheap, and selective method for fishing G‐quadruplex structures in solution by use of PDI2B and streptavidin coated magnetic beads. The new cyclic method reported leads to the recovery of more than 80 % of G‐quadruplex structures from solution, even in the presence of an excess of single‐stranded or duplex DNA as competitors. Moreover, PDI2B is a G4 ligand that…

The interaction of native DNA with Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine

The interaction of native calf thymus DNA with the Zn(II) and Cu(II) complexes of 5-triethyl ammonium methyl salicylidene orto-phenylendiimine (ZnL(2+) and CuL(2+)), in 1 mM Tris-HCl aqueous solutions at neutral pH, has been monitored as a function of the metal complex-DNA molar ratio by UV absorption spectrophotometry, circular dichroism (CD) and fluorescence spectroscopy. The results support for an intercalative interaction of both ZnL(2+) and CuL(2+) with DNA, showing CuL(2+) an affinity of approximately 10 times higher than ZnL(2+). In particular, the values of the binding constant, determined by UV spectrophotometric titration, equal to 7.3x10(4) and 1.3x10(6)M(-1), for ZnL(2+) and CuL…

Quantitative Analysis of the Interactions of Metal Complexes and Amphiphilic Systems: Calorimetric, Spectroscopic and Theoretical Aspects.

Metals and metal-based compounds have many implications in biological systems. They are involved in cellular functions, employed in the formation of metal-based drugs and present as pollutants in aqueous systems, with toxic effects for living organisms. Amphiphilic molecules also play important roles in the above bio-related fields as models of membranes, nanocarriers for drug delivery and bioremediating agents. Despite the interest in complex systems involving both metal species and surfactant aggregates, there is still insufficient knowledge regarding the quantitative aspects at the basis of their binding interactions, which are crucial for extensive comprehension of their behavior in sol…

Paracentrin 1, a synthetic antimicrobial peptide from the sea-urchin Paracentrotus lividus, interferes with staphylococcal and Pseudomonas aeruginosa biofilm formation

The rise of antibiotic-resistance as well as the reduction of investments by pharmaceutical companies in the development of new antibiotics have stimulated the investigation for alternative strategies to conventional antibiotics. Many antimicrobial peptides show a high specificity for prokaryotes and a low toxicity for eukaryotic cells and, due to their mode of action the development of resistance is considered unlikely. We recently characterized an antimicrobial peptide that was called Paracentrin 1 from the 5-kDa peptide fraction from the coelomocyte cytosol of the Paracentrotus lividus. In this study, the chemically synthesized Paracentrin 1, was tested for its antimicrobial and antibiof…

DNA-binding of zinc(II) and nickel(II) salphen-like complexes extrapolated at 1 M salt concentration: Removing the ionic strength bias in physiological conditions

Abstract The DNA-binding of two salphen-like metal complexes of nickel(II) (1) and zinc(II) (2) was investigated in different ionic strength solutions by absorption spectroscopy. The data analysis allowed us to obtain the values of their extrapolated DNA-binding constant in physiological conditions, with DNA-binding strength in the order Ni > Zn, and to give relative weight to the electrostatic and non-electrostatic contributions to their DNA-interaction.

Experimental and DFT Studies on Competitive Heterocyclic Rearrangements. A Cascade Isoxazole-1,2,4-Oxadiazole-Oxazole Rearrangement

The thermal rearrangements of 3-acylamino-5-methylisoxazoles 1 have been investigated under basic and neutral conditions and interpreted with the support of computational data. The density functional theory (DFT) study on the competitive routes available for the base-catalyzed thermal rearrangement of isoxazoles 1 showed that the Boulton-Katritzky (BK) rearrangement, producing the less stable 3-acetonyl- 1,2,4-oxadiazoles 5, is a much more favored process than either the migration-nucleophilic attack-cyclization (MNAC) or the ring contraction-ring expansion (RCRE). In turn, an increase in reaction temperature will promote the MNAC of oxadiazoles 5, producing the more stable 2-acylaminooxazo…

Thermodynamics of the Interaction between the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus-2 and the Receptor of Human Angiotensin-Converting Enzyme 2. Effects of Possible Ligands

Since the end of 2019, the coronavirus SARS-CoV-2 has caused more than 1000000 deaths all over the world and still lacks a medical treatment despite the attention of the whole scientific community. Human angiotensin-converting enzyme 2 (ACE2) was recently recognized as the transmembrane protein that serves as the point of entry of SARS-CoV-2 into cells, thus constituting the first biomolecular event leading to COVID-19 disease. Here, by means of a state-of-the-art computational approach, we propose a rational evaluation of the molecular mechanisms behind the formation of the protein complex. Moreover, the free energy of binding between ACE2 and the active receptor binding domain of the SARS…

A synchrotron radiation X-ray scattering study of aqueous solutions of native DNA

Synchrotron radiation small-angle X-ray scattering (SAXS) was used to investigate solutions of native DNA at different ionic strengths and temperatures. The mass per unit length, radius of gyration of the cross-section of DNA and apparent second virial coefficient (A2) were obtained from Zimm plots in the rodlike particle approximation. The values of A2 obtained in this way are positive and almost constant indicating that the repulsive interactions still influence the scattering patterns at resolutions as high as 5-8 nm. SAXS measurements in continuous temperature scans indicate that the rod approximation is valid over a wide temperature range during DNA melting and confirm that the rodlike…

The interaction of Schiff Base complexes of nickel(II) and zinc(II) with duplex and G-quadruplex DNA

The duplex and G-quadruplex DNA-binding of six nickel(II) and zinc(II) complexes of three salphen-like ligands (salphen = N,N?-bis-salicylidene-1,2-phenylenediaminato) was investigated by UV-visible absorption and circular dichroism spectroscopy. The results obtained, in particular the values of the DNA-binding constants, Kb, point out that the nickel(II) complexes show a higher affinity toward both duplex and G-quadruplex DNA, compared to the analogous zinc(II) complexes. Interestingly, the zinc(II) complexes possess high selectivity toward G-quadruplex DNA, being negligible their binding with duplex DNA. Molecular dynamics (MD) simulations provided atomistic models for the interpretation …

Salphen metal complexes as potential anticancer agents: interaction profile and selectivity studies toward the three G-quadruplex units in the KIT promoter

DNA G-rich sequences can organize in four-stranded structures called G-quadruplexes (G4s). These motifs are enriched in significant sites within the human genomes, including telomeres and promoters of cancer related genes. For instance, KIT proto-oncogene promoter, associated with diverse cancers, contains three adjacent G4 units, namely Kit2, SP, and Kitt. Aiming at finding new and selective G-quadruplex binders, we have synthesized and characterized five non-charged metal complexes of Pt(II), Pd(II), Ni(II), Cu(II) and Zn(II) of a chlorine substituted Salphen ligand. The crystal structure of the Pt(II) and Pd(II) complexes was determined by XRPD. FRET measurements indicated that Pt(II) an…

(Dipyrido[3,2-a:2',3'-c]phenazine)(glycinato)copper(II) perchlorate: a novel DNA-intercalator with anti-proliferative activity against thyroid cancer cell lines.

Abstract A novel copper(II) heteroleptic complex of dipyrido[3,2-a:2′,3′-c]phenazine (dppz) and glycinato (gly) as chelating ancillary ligand, [Cu(dppz)(gly)]ClO 4 ( 1 ), was synthesized and characterized. X-ray crystallography revealed that the coordination geometry of the cationic [Cu(dppz)(gly)] + unit is hexacoordinated and shows a distorted octahedral coordination geometry in the solid state, with the N,N and N,O chelating atoms of dppz and glycinato, respectively, in the square plane and in which the planar units are connected in a monodimensional polymeric array by the apical copper coordination of the second carboxylic oxygen atom. Biological assays showed that 1 exhibits a remarkab…

A novel 2,6-bis(benzoxazolyl)phenol macrocyclic chemosensor with enhanced fluorophore properties by photoinduced intramolecular proton transfer

Macrocyclic ligand L, in which a 2,6-bis(2-benzoxazolyl)phenol (bis-HBO) group is incorporated in triethylenetetramine, was designed and synthesized with the aim of creating a chemosensor with high selectivity and specificity for metal cations in an aqueous environment. The availability of several proton acceptors and donors, and amine and phenol hydroxy groups, respectively, affects the keto-enol equilibrium in both the ground and excited states, and the ligand properties show dependence on the pH of the solution. L is fluorescent in the visible range, through an excited-state intramolecular proton transfer (ESIPT) mechanism. The results of an exhaustive characterization of L by spectrosco…

Understanding the Interactions of Guanine Quadruplexes with Peptides as Novel Strategies for Diagnosis or Tuning Biological Functions

Guanine quadruplexes (G4s) are nucleic acid structures exhibiting a complex structural behavior and exerting crucial biological functions, in both cells and viruses. The specific interactions of peptides with G4s, as well as the understanding of the factors driving the specific recognition, are important for the rational design of both therapeutic and diagnostic agents. In the present minireview, we examine the most important studies dealing with the interactions between G4s and peptides, highlighting the strengths and limitations of the present analytic approaches. We also show how the combined use of high-level molecular simulation techniques and experimental spectroscopy represents the b…

DNA interaction and biological activity of first row transition metal complexes

Antiproliferative properties and g-quadruplex-binding of symmetrical naphtho[1,2-b:8,7-b’]dithiophene derivatives

Background: G-quadruplex (G4) forming sequences are recurrent in telomeres and promoter regions of several protooncogenes. In normal cells, the transient arrangements of DNA in G-tetrads may regulate replication, transcription, and translation processes. Tumors are characterized by uncontrolled cell growth and tissue invasiveness and some of them are possibly mediated by gene expression involving G-quadruplexes. The stabilization of G-quadruplex sequences with small molecules is considered a promising strategy in anticancer targeted therapy. Methods: Molecular virtual screening allowed us identifying novel symmetric bifunctionalized naphtho[1,2-b:8,7-b’]dithiophene ligands as interesting ca…

Isoxazolo[3,4-d]pyridazin-7(6H)-one derivatives endowed with anti-proliferative Activity.

Isoxazolo[3,4-d]pyridazin-7(6H)-one derivatives endowed with antiproliferative Activity B. Maggio1, G. Cancemi1, D. Raffa1, M. V. Raimondi1, F. Plescia1, A. D’Anneo2,M. Lauricella3, G. Barone4, R. Bonsignore4, G. Daidone1 1. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Medicinal Chemistry and Pharmaceutical Technologies Section, University of Palermo, ViaArchirafi 32, 90123, Palermo, Italy 2. Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, Laboratory of Biochemistry, University of Palermo. 3.Department of Experimental Biomedicine and Clinical Neurosciences, Laboratory of Biochemistry, University of Palermo. 4. Department o…

The influence of substitution in the quinoxaline nucleus on 1,3-dipolar cycloaddition reactions: A DFT study

Abstract The reaction mechanism of 1,3-dipolar cycloadditions of both symmetric and unsymmetric benzo-condensed diazines with a nitrilimine dipole, to give two different mono- and bis-cycloadducts, in tetrahydrofuran (THF) solution, was studied by DFT calculations. The results obtained show that each 1,3-dipolar cycloaddition reaction always proceeds by a two steps mechanism, in which the first intermediate shows only one covalent bond between the beta carbon of the nitrilimine and the aromatic nitrogen of the diazine molecule. The structure and energy content of the two transition states of the two cycloaddition steps, in the case of the unsymmetric benzo-condensed diazine, nicely explains…

DNA Binding and Biological Activity of Transition Metal Complexes

DHFR Inhibitors: Reading the Past for Discovering Novel Anticancer Agents.

Dihydrofolate reductase inhibitors are an important class of drugs, as evidenced by their use as antibacterial, antimalarial, antifungal, and anticancer agents. Progress in understanding the biochemical basis of mechanisms responsible for enzyme selectivity and antiproliferative effects has renewed the interest in antifolates for cancer chemotherapy and prompted the medicinal chemistry community to develop novel and selective human DHFR inhibitors, thus leading to a new generation of DHFR inhibitors. This work summarizes the mechanism of action, chemical, and anticancer profile of the DHFR inhibitors discovered in the last six years. New strategies in DHFR drug discovery are also provided, …

STUDIO DELL'INTERAZIONE DI DNA-NATIVO CON Zn(3-ACETIL-1-(2-NITROFENIL)PENTAN-1,4-DIONATO)2

DFT Calculations of the Electric Field Gradient at the Tin Nucleus as a Support of Structural Interpretation by119Sn Mössbauer Spectroscopy

DFT calculations, using an all-electron basis set and with full geometry optimization, were performed on 34 Sn(II) and Sn(IV) compounds of known structure and (119)Sn Mössbauer parameters, to obtain the theoretical values of the electric field gradient components, V(xx), V(yy), and V(zz), at the tin nucleus. These were used to determine the quantity V = V(zz)[1+ 1/3((V(xx) - V(yy))/((V(zz))(2)](1/2), for each investigated compound, which is related to the quadrupole splitting (DeltaE) parameter according to DeltaE = 1/2eQV, where e is the electronic charge and Q is the quadrupole moment of the tin nucleus. The linear fitting of the correlation plot of the experimental DeltaE, versus the cor…

DNA binding and antiproliferative activity toward human carcinoma cells of copper(ii) and zinc(ii) complexes of a 2,5-diphenyl[1,3,4]oxadiazole derivative.

The interaction of calf thymus DNA with [CuL(ClO(4))]ClO(4)·H(2)O (1) and [ZnLBr]Br·H(2)O (2) (L = 9,12,15,18,27,28-hexaaza-29-oxatetracyclo[24.2.1.0(2,7).0(20,25)]enneicosa-2,4,6,20,22,24,26,28(1)-octaene) dicationic complexes in aqueous solution at neutral pH, was investigated by variable-temperature UV-vis absorption, circular dichroism and fluorescence spectroscopy. The values of the DNA-binding constants of these complexes, determined by competitive binding spectrofluorimetric titrations of ethidium bromide (EB)-DNA solutions, are (6.7 ± 0.5) × 10(6) M(-1) for CuL(2+) and (4.7 ± 0.5) × 10(5) M(-1) for ZnL(2+). These data together with a through analysis of the spectroscopic behaviour c…

The Right Answer for the Right Electrostatics: Force Field Methods Are Able to Describe Relative Energies of DNA Guanine Quadruplexes

Different force fields and approximate density functional theory were applied in order to study the rotamer space of the telomeric G-quadruplex DNA. While some force fields show an erratic behavior when it comes to the reproduction of the higher-order DNA conformer space, OPLS and MMFF implementations are able to reproduce the experimentally known energy order. The stabilizing effect of the AA (anti−anti) versus SA (syn−anti) conformer is analyzed applying mechanical bond strength descriptors (compliance constants). The fact that we observe the correct energy order using appropriate force fields is in contrast with results previously reported, which suggested the general inappropriateness o…

2-Methoxyestradiol Affects Mitochondrial Biogenesis Pathway and Succinate Dehydrogenase Complex Flavoprotein Subunit A in Osteosarcoma Cancer Cells.

Background/aim Dysregulation of mitochondrial pathways is implicated in several diseases, including cancer. Notably, mitochondrial respiration and mitochondrial biogenesis are favored in some invasive cancer cells, such as osteosarcoma. Hence, the aim of the current work was to investigate the effects of 2-methoxyestradiol (2-ME), a potent anticancer agent, on the mitochondrial biogenesis of osteosarcoma cells. Materials and methods Highly metastatic osteosarcoma 143B cells were treated with 2-ME separately or in combination with L-lactate, or with the solvent (non-treated control cells). Protein levels of α-syntrophin and peroxisome proliferator-activated receptor gamma, coactivator 1 alph…

Quantum chemical models of acidic sites in H-ZSM-5 zeolites

Interaction of Cd(II) and Ni(II) terpyridine complexes with model polynucleotides: A multidisciplinary approach

Two metal complexes of 2,2′:6′,2′′-terpyridine (terpy), i.e. Cd(terpy)Cl2 and Ni(terpy)Cl2·3H2O, have been prepared and extensively characterized. The interaction of Cd(terpy)Cl2 with synthetic DNA models, poly(dA-dT)·poly(dA-dT) (polyAT) and poly(dG-dC)·poly(dG-dC) (polyGC), has been studied by CD, fluorescence and UV-vis electronic absorption spectroscopy at several metal/polynucleotide–phosphate ratios and for different NaCl concentrations. All the experimental results indicate an intercalative mechanism of interaction. The optimized geometry of the cadmium complex intercalated between the sixth and seventh base pairs of (AT) and (GC) dodecanucleotide duplexes, obtained by quantum mechan…

Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity

The affinity of three square-planar nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff-base complexes for wild-type human telomeric (h-Telo) and protooncogene c-myc G-quadruplex (G4) DNA was investigated by UV-visible absorption spectroscopy and circular dichroism. DNA-binding constants (Kb) were determined by spectrophotometric titrations for both G4-DNA and B-DNA. The results obtained point out that the three metal complexes selectively bind G4-DNA with higher affinity, up to two orders of magnitude, with respect to B-DNA. The nickel(II) complex 1 was found to be the most effective G4-DNA stabilizer and the Kb values decrease in the order 1 > 2 ≈ 3. Innovative computational investigat…

Synthesis, characterization, and in vitro antimicrobial activity of organotin(IV) complexes with triazolo-pyrimidine ligands containing exocyclic oxygen atoms

Abstract Tri-organotin(IV) complexes of the triazolo-pyrimidine derivatives 4,5-dihydro-5-oxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (5HtpO), 4,7-dihydro-5-methyl-7-oxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (HmtpO), and 4,5,6,7-tetrahydro-5,7-dioxo-[1,2,4]triazolo-[1,5 a ]pyrimidine (H 2 tpO 2 ), and the diorganotin derivative n -Bu 2 Sn(tpO 2 ), were synthesized and characterized by means of infrared and 119 Sn Mossbauer spectroscopy. In all the complexes obtained the triazolopyrimidines act as multidentate ligands producing polymeric structures. A trigonal bipyramidal arrangement of the ligands around the tin atom is proposed for triorganotin(IV) derivatives, with organic groups on the equatoria…

On the G‐quadruplex binding of a new class of Ni(II), Cu(II) and Zn(II) salphen‐like complexes

The involvement of non-canonical DNA structures, such as Gquadruplex (G4) DNA, in cancer development and progression has set the pace towards the renaissance of DNA-binding metal complexes. In this work, we report the DNA-binding of three Ni(II), Cu(II), Zn(II) complexes of a salphen-like N4-donor ligand, bearing two imidazole groups condensed with a phenylenediamine moiety. Both duplex and G4 DNAs derived from human telomeres (hTelo), and a sequence mimicking the promoter of the oncogene myc (c-myc) were studied. UV-Vis and circular dichroism spectroscopic binding studies pointed out that, while all the three complexes bind the selected oligonucleotides, the Cu(II) derivative is the strong…

Teaching Inorganic Photophysics and Photochemistry with Three Ruthenium(II) Polypyridyl Complexes: A Computer-Based Exercise

Among computational methods, DFT (density functional theory) and TD-DFT (time-dependent DFT) are widely used in research to describe, inter alia, the optical properties of transition metal complexes. Inorganic/physical chemistry courses for undergraduate students treat such methods, but quite often only from the theoretical point of view. In the calculation exercise herein described, students are guided step by step through the computational study of the photophysics and photochemistry of polypyridyl Ru(II) d6-metal complexes. In particular, by means of DFT and TD-DFT calculations, they are asked to examine and interpret a set of experimental data describing the absorption, emission, and ph…

Ab initio study of structure and energetics of species involved in the 2,4-dinitro-toluene hydrogenation on Pd catalysts

Abstract Quantum-mechanical calculations, at HF level, were performed to gain chemical–physical basis information on the 2,4-dinitro-toluene hydrogenation occurring over palladium catalysts. To investigate the surface characteristics of the species involved in the reaction system, simplified molecular models including small metal clusters were considered. Remarkable findings, useful to elucidate the reaction mechanism and important parameters, working in time dependent Monte-Carlo simulations of the title reaction, were obtained; inter alia: the molar standard free energies of the molecules involved in the reaction, the volume occupied by the species in solution phase and the qualitative or…

Interaction of Doxorubicin with Polynucleotides. A Spectroscopic Study

The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (polyAT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV-vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.

Quaternary structures of GroEL and naïve-Hsp60 chaperonins in solution: a combined SAXS-MD study

The quaternary structures of bacterial GroEL and human naïve-Hsp60 chaperonins in physiological conditions have been investigated by an innovative approach based on a combination of synchrotron Small Angle X-ray Scattering (SAXS) in-solution experiments and molecular dynamics (MD) simulations. Low-resolution SAXS experiments over large and highly symmetric oligomers are analyzed on the basis of the high-resolution structure of the asymmetric protein monomers, provided by MD. The results reveal remarkable differences between the solution and the crystallographic structure of GroEL and between the solution structures of GroEL and of its human homologue Hsp60.

The potential of antimicrobial peptides isolated from freshwater crayfish species in new drug development: A review

Abstract The much-publicised increased resistance of pathogenic bacteria to conventional antibiotics has focused research effort on the characterization of new antimicrobial drugs. In this context, antimicrobial peptides (AMPs) extracted from animals are considered a promising alternative to conventional antibiotics. In recent years, freshwater crayfish species have emerged as an important source of bioactive compounds. In fact, these invertebrates rely on an innate immune system based on cellular responses and on the production of important effectors in the haemolymph, such as AMPs, which are produced and stored in granules in haemocytes and released after stimulation. These effectors are …

Induction of 2-hydroxycatecholestrogens O-methylation: A missing puzzle piece in diagnostics and treatment of lung cancer

Lung cancer is one of the most common cancers worldwide, causing nearly one million deaths each year. Herein, we present the effect of 2-methoxyestradiol (2-ME), the endogenous metabolite of 17β-estradiol (E2), on non-small cell lung cancer (NSCLC) cells. We observed that 2-ME reduced the viability of lung adenocarcinoma in two-dimensional (2D) and three-dimensional (3D) spheroidal A549 cell culture models. Molecular modeling was carried out aiming to visualize amino acid residues within binding pockets of the acyl-protein thioesterases, namely 1 (APT1) and 2 (APT2), and thus to identify which ones were more likely involved in the interaction with 2-ME. Our findings suggest that 2-ME acts a…

Identification of New Antimicrobial Peptides from Mediterranean Medical Plant Charybdis pancration (Steinh.) Speta

The present work was designed to identify and characterize novel antimicrobial peptides (AMPs) from Charybdis pancration (Steinh.) Speta, previously named Urginea maritima, is a Mediterranean plant, well-known for its biological properties in traditional medicine. Polypeptide-enriched extracts from different parts of the plant (roots, leaves and bulb), never studied before, were tested against two relevant pathogens, Staphylococcus aureus and Pseudomonas aeruginosa. With the aim of identifying novel natural AMPs, peptide fraction displaying antimicrobial activity (the bulb) that showed minimum inhibitory concentration (MICs) equal to 30 &micro

Erratum to “New time-dependent Monte Carlo algorithm designed to model three-phase batch reactor processes: applications on 2,4-dinitro-toluene hydrogenation on Pd/C catalysts” [Chem. Eng. J. 91 (2003) 133–142]

Erratum to “New time-dependent Monte Carlo algorithm designed to model three-phase batch reactor processes: applications on 2,4-dinitro-toluene hydrogenation on Pd/C catalysts” [Chem. Eng. J. 91 (2003) 133–142] Giampaolo Barone a,b, Dario Duca a,b,∗ a Dipartimento di Chimica Inorganica ed Analitica, Universita di Palermo, Viale delle Scienze, I-90128 Palermo, Italy b Dipartimento di Scienze Farmaceutiche, Universita di Salerno, Via Ponte don Melillo, I-84084 Fisciano, Salerno, Italy

Synthesis and chemical characterization of CuII, NiII and ZnII complexes of 3,5-bis(20-pyridyl)-1,2,4-oxadiazole and 3-(20-pyridyl)5-(phenyl)-1,2,4-oxadiazole ligands

The synthesis and structural characterization of NiII, CuII and ZnII complexes of two chelating 1,2, 4-oxadiazole ligands, namely 3,5-bis(20-pyridyl)-1,2,4-oxadiazole (bipyOXA) and 3-(20-pyridyl)5- (phenyl)-1,2,4-oxadiazole (pyOXA), is here reported. The formed hexacoordinated metal complexes are [M(bipyOXA)2(H2O)2](ClO4)2 and [M(pyOXA)2(ClO4)2], respectively (M = Ni, Cu, Zn). X-ray crystallography, 1H and 13C NMR spectroscopy and C, N, H elemental analysis data concord in attributing them an octahedral coordination geometry. The two coordinated pyOXA ligands assume a trans coplanar disposition, while the two bipyOXA ligands are not. The latter result is a possible consequence of the format…

C−C Cross-Couplings from a Cyclometalated Au(III) C∧ N Complex: Mechanistic Insights and Synthetic Developments

Abstract In recent years, the reactivity of gold complexes was shown to extend well beyond π‐activation and to hold promises to achieve selective cross‐couplings in several C−C and C−E (E=heteroatom) bond forming reactions. Here, with the aim of exploiting new organometallic species for cross‐coupling reactions, we report on the Au(III)‐mediated C(sp2)−C(sp) occurring upon reaction of the cyclometalated complex [Au(CCH2N)Cl2] (1, CCH2N=2‐benzylpyridine) with AgPhCC. The reaction progress has been monitored by NMR spectroscopy, demonstrating the involvement of a number of key intermediates, whose structures have been unambiguously ascertained through 1D and 2D NMR analyses (1H, 13C, 1H‐1H CO…

A synthetic derivative of antimicrobial peptide holothuroidin 2 from mediterranean sea cucumber (Holothuria tubulosa) in the control of Listeria monocytogenes

Due to the limited number of available antibiotics, antimicrobial peptides (AMPs) are considered antimicrobial candidates to fight difficult-to-treat infections such as those associated with biofilms. Marine environments are precious sources of AMPs, as shown by the recent discovery of antibiofilm properties of Holothuroidin 2 (H2), an AMP produced by the Mediterranean sea cucumber Holothuria tubulosa. In this study, we considered the properties of a new H2 derivative, named H2d, and we tested it against seven strains of the dangerous foodborne pathogen Listeria monocytogenes. This peptide was more active than H2 in inhibiting the growth of planktonic L. monocytogenes and was able to interf…

Complessi metaliici e DNA nativo: interazione di intercalazione

Structural and Kinetic DFT Characterization of Materials to Rationalize Catalytic Performance

This review shortly discusses recent results obtained by the application of density functional theory for the calculations of the adsorption and diffusion properties of small molecules and their reactivity on heterogenous catalytic systems, in the ambit of the Nanocat project. Particular focus has been devoted to palladium catalysts, either in atomic or small cluster form. Some protocols have been tested to obtain efficient ways able to treat the electronic and geometric influence of supports like zeolites and carbon nanotubes on the catalytic properties of palladium. The hydroisomerization of cis-but-2-ene is discussed as model reaction on supported and unsupported Pd clusters. Some prelim…

Ground state and electronic spectrum of Cu(ii) and Cu(iii) complexes of N,N′-1,2-phenylenebis-2-mercaptoacetamide

The electronic structure and the UV-vis spectrum of reduced and oxidized model systems of the N,N'-1,2-phenylenebis(2-mercapto-2-methylpropionamide) copper complex have been studied using a multiconfigurational quantum chemical method (CASSCF/CASPT2). The bonds between Cu and the two sulfur ligand atoms have a large covalent character in the oxidized Cu(III) form. As a result of the increased covalency, the effective charge on the Cu atom is actually smaller in the oxidized form. The electronic spectrum for both oxidation states of the complex is in agreement with the experiment for excitation energies and intensities showing that the theoretical description of the electronic structure is e…

Studio computazionale della interazione tra proflavina e i polinucleotidi poly(dA-dT).poly(dA-dT) e poly(dG-dC).poly(dG-dC).

Experimental and DFT Studies on Competitive Heterocyclic Rearrangements. Part 2:1 A One-Atom Side-Chain versus the Classic Three-Atom Side-Chain (Boulton−Katritzky) Ring Rearrangement of 3-Acylamino-1,2,4-oxadiazoles

The experimental investigation of the base-catalyzed rearrangements of 3-acylamino-1,2,4-oxadiazoles evidenced a new reaction pathway which competes with the well-known ring-degenerate Boulton-Katritzky rearrangement (BKR). The new reaction consists of a one-atom side-chain rearrangement that is base-activated, occurs at a higher temperature than the BKR, and irreversibly leads to the corresponding 2-acylamino-1,3,4-oxadiazoles. An extensive DFT study is reported to elucidate the proposed reaction mechanism and to compare the three possible inherent routes: (i) the reversible three-atom side-chain ring-degenerate BKR, (ii) the ring contraction-ring expansion route (RCRE), and (iii) the one-…

1,3-Dipolar cycloadditions with meso-tetraarylchlorins – site selectivity and mixed bisadducts

The 1,3-dipolar cycloaddition reaction of meso-tetraarylporphyrins with nitrones gives isoxazolidine-fused chlorins. Depending on the substitution pattern on the meso-aryl groups and the nitrone, the chlorins can be obtained in high yields (up to 91%). Bacteriochlorin-type bisadducts are also obtained, although in low yield, from the reaction of meso-tetrakis(pentafluorophenyl)porphyrin with N-methyl, N-cyclohexyl or N-benzyl nitrone. The structure of a bis(N-benzyl isoxazolidine-fused) bacteriochlorin was determined by single-crystal X-ray diffraction and rationalized by DFT calculations. To further explore the nature of site selectivity in the formation of bisadducts, isomeric mixed bacte…

Experimental and DFT Studies on Competitive Heterocyclic Rearrangements. 3. A Cascade Isoxazole−1,2,4-Oxadiazole−Oxazole Rearrangement

The thermal rearrangements of 3-acylamino-5-methylisoxazoles 1 have been investigated under basic and neutral conditions and interpreted with the support of computational data. The density functional theory (DFT) study on the competitive routes available for the base-catalyzed thermal rearrangement of isoxazoles 1 showed that the Boulton-Katritzky (BK) rearrangement, producing the less stable 3-acetonyl-1,2,4-oxadiazoles 5, is a much more favored process than either the migration-nucleophilic attack-cyclization (MNAC) or the ring contraction-ring expansion (RCRE). In turn, an increase in reaction temperature will promote the MNAC of oxadiazoles 5, producing the more stable 2-acylaminooxazol…

Spectroscopic Study of the Interaction of NiII-5-triethyl Ammonium Methyl Salicylidene orto-phenylendiiminato with Native DNA

CASSCF/CASPT2 analysis of the fragmentation of H2 on a Pd4 cluster

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

Specific Recognition of the 5′-Untranslated Region of West Nile Virus Genome by Human Innate Immune System

In the last few years, the sudden outbreak of COVID-19 caused by SARS-CoV-2 proved the crucial importance of understanding how emerging viruses work and proliferate, in order to avoid the repetition of such a dramatic sanitary situation with unprecedented social and economic costs. West Nile Virus is a mosquito-borne pathogen that can spread to humans and induce severe neurological problems. This RNA virus caused recent remarkable outbreaks, notably in Europe, highlighting the need to investigate the molecular mechanisms of its infection process in order to design and propose efficient antivirals. Here, we resort to all-atom Molecular Dynamics simulations to characterize the structure of th…

Silver Clusters of Five Atoms as Highly Selective Antitumoral Agents Through Irreversible Oxidation of Thiols

Low atomicity clusters present properties dependent on the size, due to the quantum confinement, with well-defined electronic structures and high stability. Here it is shown that Ag5 clusters catalyze the complete oxidation of sulfur to S+6. Ag5 catalytic activity increases with different oxidant species in the order O2 ≪ H2O2 < OH•. Selective oxidation of thiols on the cysteine residues of glutathione and thioredoxin is the primary mechanism human cells have to maintain redox homeostasis. Contingent upon oxidant concentration, Ag5 catalyzes the irreversible oxidation of glutathione and thioredoxin, triggering apoptosis. Modification of the intracellular environment to a more oxidized state…

New time-dependent Monte Carlo algorithm designed to model three-phase batch reactor processes: applications on 2,4-dinitro-toluene hydrogenation on Pd/C catalysts

Abstract The hydrogenation of 2,4-dinitro-toluene on a Pd/C catalyst was employed as a test reaction to simulate, by the time-dependent Monte Carlo method, processes occurring in a three-phase batch reactor working at isobar and isotherm conditions. A new time-dependent Monte Carlo algorithm, including an original subroutine useful to reduce the time of the simulations, was developed and implemented in Fortran language. The paper describes the flowchart of the code together with the main technical details and the involved physical and chemical models. Computational characteristics, such as the simulated time to reach surface steady state conditions and the effects of the catalyst morphology…

Structural distortions in homoleptic (RE)4A (E = O, S, Se; A = C, Si, Ge, Sn): Implications for the CVD of tin sulfides

The structures of Sn(SBut)4 and Sn(SCy)4 have been determined and adopt S4 and D2 conformations respectively; the anion [(PhS)Sn3]−, as its Ph4P+ salt, has a structure approaching Cs symmetry. In all three compounds, there are large variations in the ∠S–Sn–S within the same molecule, which have been rationalised in terms of the C–S–Sn–S–C conformations. For Sn(SR)4, the ∠S–Sn–S increases as the conformations change from trans, trans to trans, gauche and gauche, gauche, as the number of eclipsed lone pairs decreases and this rationale is shown to be applicable to a variety of A(ER)4 (A = C, Si, Ge, Sn; E = O, S, Se) and related [Mo(SR)4, Ga(SR)4−] systems. AM1 calculations have been used to …

DNA Binding Studies and Cytotoxicity of a Dinuclear PtII Diazapyrenium- Based Metallo-supramolecular Rectangular Box

The interaction with native DNA of a 2,7-diazapyrenium-based ligand 1 and its Pt II rectangular metal- lacycle 2 is explored through circular and linear dichroism and fluorescence spectroscopies. The metal-free ligand 1 binds through intercalation, with a binding constant of approximately 5 � 10 5 m � 1 , whereas the metallacycle 2 binds and bends the DNA with a bind- ing constant of 7 � 10 6 m � 1 . PCR assays show that metallo-supramolecular box 2 interferes with DNA transactions in vitro whereas the intercalator 1 does not. The metallacycle is active against four human cancer cell lines, with IC50 values ranging between 3.1 and 19.2 mm and shows similar levels of efficacy, but a differen…

ChemInform Abstract: Pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine: A New Ring System Through Dimroth Rearrangement.

Abstract Derivatives of the new ring system pyrazolo[3,4- d ][1,2,3]triazolo[1,5- a ]pyrimidine were synthesized from the corresponding angular isomers, through a Dimroth rearrangement, in quantitative yields. Preliminary computational studies demonstrated that this class of compounds could be a good candidate as DNA intercalating agents.

Nickel(II), copper(II) and zinc(II) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation

We present a thorough characterization of the interaction of novel nickel(II) (1), copper(II) (2) and zinc(II) (3) Schiff base complexes with native calf thymus DNA (ct-DNA), in buffered aqueous solution at pH 7.5. UV-vis absorption, circular dichroism (CD) and viscometry titrations provided clear evidence of the intercalative mechanism of the three square-planar metal complexes, allowing us to determine the intrinsic DNA-binding constants (K(b)), equal to 1.3 × 10(7), 2.9 × 10(6), and 6.2 × 10(5) M(-1) for 1, 2 and 3, respectively. Preferential affinity, of one order of magnitude, toward AT compared to GC base pair sequences was detected by UV-vis absorption titrations of 1 with [poly(dG-d…

A novel compound of triphenyltin(IV) with N-tert-butoxycarbonyl-L-ornithine causes cancer cell death by inducing a p53-dependent activation of the mitochondrial pathway of apoptosis

The triphenyltin(IV) compound with N-tert-butoxycarbonyl-L-ornithine (Boc-Orn-OH), [Ph3Sn(Boc-Orn-O)], was synthesized and characterized by elemental analysis, FT-IR, solution1H,13C and119Sn NMR and ESI mass spectrometry. The organotin(IV) compound inhibited at very low micromolar concentrations the growth of human tumor cell lines HepG2 (hepatocarcinoma cells), MCF-7 (mammary cancer) and HCT116 (colorectal carcinoma) while it did not affect the viability of non-malignant human-derived hepatic cells Chang. The mechanism of the antiproliferative effect of Ph3Sn(Boc-Orn-O), investigated on human hepatoma HepG2 cells, was pro-apoptotic, being associated with externalization of plasma membrane …

NiII, and ZnII Schiff Base Complexes: Telomeric G-quadruplex Stabilizers

Recently, NiII and ZnII metal complexes of the ligand Salpyrim have been synthesized and characterized. Their affinity for wild-type h-Telo G-quadruplex DNA and for calf thymus DNA was investigated by UV absorption spectroscopy, circular dichroism and viscometry. The data collectively suggest that both complexes bind effectively to G-quadruplexes by direct end-stacking, stabilizing the oligonucleotide secondary structure. The two complexes are also typical B-DNA intercalators. Remarkably, their binding constants, Kb, with the G4s structures are about 10 fold higher than those with B-DNA, highlighting the selectivity. Experiments to evaluate the biological activity of the two complexes again…

Antimicrobial and Antibiofilm Activity of a Recombinant Fragment of β-Thymosin of Sea Urchin Paracentrotus lividus

With the aim to obtain new antimicrobials against important pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa, we focused on antimicrobial peptides (AMPs) from Echinoderms. An example of such peptides is Paracentrin 1 (SP1), a chemically synthesised peptide fragment of a sea urchin thymosin. In the present paper, we report on the biological activity of a Paracentrin 1 derivative obtained by recombination. The recombinant paracentrin RP1, in comparison to the synthetic SP1, is 22 amino acids longer and it was considerably more active against the planktonic forms of S. aureus ATCC 25923 and P. aeruginosa ATCC 15442 at concentrations of 50 &micro

PREDICTION OF MOESSBAUER PARAMETERS IN A DOUGLAS–KROLL–HESS FRAMEWORK

Sintesi di Nuovi Derivati del Sistema Triciclico Pirazolo[3,4-d][1,2,3]triazolo[1,5-a]pirimidinico DNA interattivi

The prediction of the nuclear quadrupole splitting of 119Sn Mössbauer spectroscopy data by scalar relativistic DFT calculations.

The electric field gradient components for the tin nucleus of 34 tin compounds of experimentally known structures and Sn-119 Mossbauer spectroscopy parameters were computed at the scalar relativistic density functional theory level of approximation. The theoretical values of the electric field gradient components were used to determine a quantity, V, which is proportional to the nuclear quadrupole splitting parameter (Delta E). In a subsequent linear regression analysis the effective nuclear quadrupole moment, Q, was evaluated. The value of (11.9 +/- 0.1) fm(2) is a significant improvement over the non-relativistic result of (15.2 +/- 4.4) fm(2) and is in agreement with the experimental val…

Structure and Stability of Hsp60 and Groel in Solution

Molecular chaperones are a class of proteins able to prevent non-specific aggregation of mitochondrial proteins and to promote their proper folding. Among them, human Hsp60 is currently considered as a ubiquitous molecule with multiple roles both in maintaining health conditions and as a trigger of several diseases. Of particular interest is its role in neurodegenerative disorders since it is able to inhibit the formation of amyloid fibrils.Hsp60 structure was considered, until recent years, analogue to the one of its bacterial homolog GroEL, one of the most investigated chaperones, whose crystallographic structure is a homo-tetradecamer, made up of two seven member rings. On the contrary, …

Attività anti-proliferativa di derivati di organostagno(IV) con Na-Boc-Ornitina e studio dell’azione pro-apoptotica del derivato Ph3Sn(Boc- Orn)

Nuovi composti di organostagno(IV) [R3SnL e R¢2SnL2 (R = Me, Ph e R¢= Me, nBu, HL= Na-Boc-Ornitina)] sono stati sintetizzati e caratterizzati sia allo stato solido (FT-IR) che in soluzione (1H e 13C NMR) per poterne valutare la citotossicità in linee cellulari tumorali [1]. Na-Boc-Ornitina si comporta come un legante chelante dello stagno con il gruppo carbossilato, mentre il gruppo amminico Na-protetto è esente dalla coordinazione. I composti sono stati testati per l’attività citotossica in vitro su cellule neoplastiche umane HepG2 di epatocarcinoma ed MCF7 di cancro al seno. L’effetto dei composti, nel range da 0.5 a 25 μM, dopo 24 h di incubazione è stato valutato mediante saggio MTT. Il…

Modification of DNA structure by reactive nitrogen species as a result of 2-methoxyestradiol–induced neuronal nitric oxide synthase uncoupling in metastatic osteosarcoma cells

Abstract 2-methoxyestradiol (2-ME) is a physiological anticancer compound, metabolite of 17β-estradiol. Previously, our group evidenced that from mechanistic point of view one of anticancer mechanisms of action of 2-ME is specific induction and nuclear hijacking of neuronal nitric oxide synthase (nNOS), resulting in local generation of nitro-oxidative stress and finally, cancer cell death. The current study aims to establish the substantial mechanism of generation of reactive nitrogen species by 2-ME. We further achieved to identify the specific reactive nitrogen species involved in DNA-damaging mechanism of 2-ME. The study was performed using metastatic osteosarcoma 143B cells. We detected…

Multivariate analysis in the identification of biological targets for designed molecular structures: The BIOTA protocol

In this work the new protocol BIOlogical Target Assignation (BIOTA) for the prediction of the biological target from molecular structures is proposed. BIOTA is based on the Principal Components Analysis (PCA) application on a matrix of ligands versus molecular descriptors. The application of BIOTA could allow to hypothesize the mechanism of action of a candidate drug prior to its biological evaluation or to repurpose old drugs. The protocol can be fine-tuned by choosing opportune targets (biological or not) and molecular descriptors, and it can be useful in every fields in with it is possible to collect set of compounds with known properties. The robustness of the protocol depends from diff…

H−ZSM-5 Modified Zeolite:  Quantum Chemical Models of Acidic Sites

A ZSM-5 fragment, containing 52 tetrahedral moieties, each of them formed by one silicon or one aluminum atom surrounded by four oxygen atoms, was employed to model (52T systems) by quantum chemical calculations (i) the influence of the positions of the acidic sites on the energetics of 22 aluminum monosubstituted and bisubstituted 52T acidic zeolite (H-ZSM-5) systems and (ii) the local adsorption properties and acidic strength of the corresponding -OH sites. The energetics and the structural properties of simpler acid H-ZSM-5 systems containing only five Tetrahedral moieties (5T systems) were also modeled for comparison. B3LYP/6-31G(d,p) partial geometry optimization routines were performe…

The interaction of S,N-coordinated dimethyltin(IV) derivatives with deoxyribonucleic acid: structure and dynamics by119Sn Mössbauer spectroscopy

Complexes Me2SnCl(SPy) and Me2SnCl(SPym) (HSPy = 2-mercaptopyridine; HSPym = 2-mercaptopyrimidine), from ethanol solutions, interact with aqueous calf-thymus DNA yielding condensed phases with probable Me2Sn(SPy,SPym) (DNA monomer) stoichiometries of 1:1; the condensation of DNA is inferred originated from electrostatic bonding between complex cations Me2Sn(SPy,SPym)+ and the phosphate oxygen of the phosphodiester groups. Octahedral-or trigonal-bipyramidal tin environments are inferred from the point-charge model treatment of the 119Sn Mossbauer parameter nuclear quadrupole splitting, considering the bonding by S and N, or only S donor atoms from the ligand, as well as possible coordination…

Zinc complexes as fluorescent chemosensors for nucleic acids: new perspectives for a “boring” element

Zinc(ii) complexes are effective and selective nucleic acid-binders and strongly fluorescent molecules in the low energy range, from the visible to the near infrared. These two properties have often been exploited to quantitatively detect nucleic acids in biological samples, in both in vitro and in vivo models. In particular, the fluorescent emission of several zinc(ii) complexes is drastically enhanced or quenched by the binding to nucleic acids and/or upon visible light exposure, in a different fashion in bulk solution and when bound to DNA. The twofold objective of this perspective is (1) to review recent utilisations of zinc(ii) complexes as selective fluorescent probes for nucleic acid…

Pyrrolomycins as antimicrobial agents. Microwave-assisted organic synthesis and insights into their antimicrobial mechanism of action

Abstract New compounds able to counteract staphylococcal biofilm formation are needed. In this study we investigate the mechanism of action of pyrrolomycins, whose potential as antimicrobial agents has been demonstrated. We performed a new efficient and easy method to use microwave organic synthesis suitable for obtaining pyrrolomycins in good yields and in suitable amount for their in vitro in-depth investigation. We evaluate the inhibitory activity towards Sortase A (SrtA), a transpeptidase responsible for covalent anchoring in Gram-positive peptidoglycan of many surface proteins involved in adhesion and in biofilm formation. All compounds show a good inhibitory activity toward SrtA, havi…

Quantum dots functionalised artificial peptides bioinspired to the D1 protein from the Photosystem II of Chlamydomonas reinhardtii for endocrine disruptor optosensing

Herein we describe the design and synthesis of novel artificial peptides mimicking the plastoquinone binding niche of the D1 protein from the green photosynthetic alga Chlamydomonas reinhardtii, also able to bind herbicides. In particular, molecular dynamics (MD) simulations were performed to model in silico the behaviour of three peptides, D1Pep70-H, D1Pep70-S264K and D1Pep70-S268C, as genetic variants with different affinity towards the photosynthetic herbicide atrazine. Then the photosynthetic peptides were functionalised with quantum dots for the development of a hybrid optosensor for the detection of atrazine, one of the most employed herbicides for weed control in agriculture as well …

DNA-binding of nickel(II), copper(II) and zinc(II) complexes: structure-affinity relationships

Abstract Nickel(II), copper(II) and zinc(II) complexes with the same ligands normally display analogous coordination geometry and binding mode toward DNA. However, although qualitatively alike in structure and properties, different DNA-binding ability has often been observed. This review surveys the most recent examples of binding of the three metal ions complexed with monodentate and chelating bidentate to tetradentate ligands to DNA. An attempt has also been made to rationalize the observed trend in the values of the intrinsic DNA-binding constant, Kb, in terms of structural and chemical features.

The interaction of native calf thymus DNA with Zn(II)-N,N'-bis(5,5'-triethylammoniomethyl-salicylidene)phenylendiimine

The interaction between native calf thymus deoxyribonucleic acid (DNA) and Fe-III-N,N'-ethylene-bis (salicylideneiminato)chloride, Fe(Salen)Cl, was investigated in aqueous solutions by UV-visible (UV-vis) absorption, circular clichroisin (CD), thermal denaturation and viscosity measurements. The results obtained from CD, UV-vis and viscosity measurements exclude DNA intercalation and can be interpreted in terms of an electrostatic binding between the Fe(Salen)(+) cation and the phosphate groups of DNA. The trend of the UV-vis absorption band of the Fe(Salen)Cl complex at different ratios [DNA(phosphate)]/[Fe(Salen)Cl] and the large increase of the melting temperature of DNA in the presence …

The Binding Mechanism of Epolactaene to Hsp60 Unveiled by in Silico Modelling

Molecular Dynamics (MD) simulations and DFT/MM calculations were performed in order to rationalize available experimental results and to provide structural details on the binding mechanism of Epolactaene (EPO) to the 60 KDa Heat Shock Protein (Hsp60). The available crystal structure of Hsp60 represents the last step of the chaperone folding cycle, while the Hsp60-EPO complex was obtained by using a homology model of Hsp60, in order to simulate a state related to the beginning of the folding cycle (Rs1). The results of MD simulations point out that EPO shows the highest binding affinity for the empty ATP binding site. The presence of ATP opens a channel that allows the entrance of both EPO d…

Experimental and DFT studies on competitive heterocyclic rearrangements. part 2: A one-atom side-chain versus the classic three-atom side-chain (Boulton-Katritzky) ring rearrangement of 3-acylamino-1,2,4-oxadiazoles

The experimental investigation of the base-catalyzed rearrangements of 3-acylamino-1,2,4-oxadiazoles evidenced a new reaction pathway which competes with the well-known ring-degenerate Boulton- Katritzky rearrangement (BKR). The new reaction consists of a one-atom side-chain rearrangement that is base-activated, occurs at a higher temperature than the BKR, and irreversibly leads to the corresponding 2-acylamino-1,3,4-oxadiazoles. An extensive DFT study is reported to elucidate the proposed reaction mechanism and to compare the three possible inherent routes: (i) the reversible three-atom side-chain ring-degenerate BKR, (ii) the ring contraction-ring expansion route (RCRE), and (iii) the one…

Computational study of dimethyl- and trimethyl-tin(IV) complexes of porphyrin derivatives

The molecular geometry, energetics and electronic charge distribution of diorgano- and triorgano-tin(IV) complexes of [protoporphyrin-IX] and [meso-tetra(4-carboxyphenyl)porphine] derivatives were determined at semi-empirical and ab initio levels. To study the molecular details of the complexes, simpler molecule models were calculated by the ab initio pseudo-potential method. The molecular properties of these complexes are essentially independent of the presence of the peripheral tin atoms. Agreement was always found among the results of the different computational approaches, as well as between the theoretical and the experimental findings on the molecular geometry of the hypothesized comp…

Analytic high-order Douglas–Kroll–Hess electric field gradients

In this work we present a comprehensive study of analytical electric field gradients in hydrogen halides calculated within the high-order Douglas-Kroll-Hess (DKH) scalar-relativistic approach taking picture-change effects analytically into account. We demonstrate the technical feasibility and reliability of a high-order DKH unitary transformation for the property integrals. The convergence behavior of the DKH property expansion is discussed close to the basis set limit and conditions ensuring picture-change-corrected results are determined. Numerical results are presented, which show that the DKH property expansion converges rapidly toward the reference values provided by four-component met…

Synthesis and thermal decomposition studies of homo- and heteroleptic tin(iv) thiolates and dithiocarbamates: molecular precursors for tin sulfides

The syntheses and X-ray structures of novel heteroleptic thiolate/dithiocarbamate derivatives (Et2NCS2)2(RS)2Sn (R = Cy, CH2CF3) have been examined and their thermal decompositions compared with those of selected tin(II) and tin(IV) dithiocarbamates. The heteroleptic species decompose to SnS by initial elimination of RSSR to afford (Et2NCS2)2Sn and subsequent loss of [Et2NC(S)]2S. In contrast, (Et2NCS2)4Sn decomposes via [(Et2NCS2)2SnS]2, whose structure has been determined, and finally to SnS2 by sequential elimination of [Et2NC(S)]2S. The two families of compounds, (R2NCS2)4Sn and (Et2NCS2)2(RS)2Sn, thus provide single-source materials for bulk SnS2 and SnS, respectively, by virtue of the…

Nanomedicine: Silver Atomic Quantum Clusters of Three Atoms for Cancer Therapy: Targeting Chromatin Compaction to Increase the Therapeutic Index of Chemotherapy (Adv. Mater. 33/2018)

Pyrazolo[3,4-d][1,2,3]triazolo[1,5-a]pyrimidine: a new ring system through Dimroth rearrangement

Abstract Derivatives of the new ring system pyrazolo[3,4- d ][1,2,3]triazolo[1,5- a ]pyrimidine were synthesized from the corresponding angular isomers, through a Dimroth rearrangement, in quantitative yields. Preliminary computational studies demonstrated that this class of compounds could be a good candidate as DNA intercalating agents.

Intercalation of daunomycin into stacked DNA base pairs. DFT study of an anticancer drug

We have computationally studied the intercalation of the antitumor drug daunomycin into six stacks of Watson-Crick DNA base pairs i.e., AT-AT, AT-TA, GC-AT, CG-TA, GC-GC, GC-CG) using density functional theory (DFT). The proton affinity of the DNA intercalater daunomycin in water was computed to be 159.2 kcal/mol at BP86/TZ2P, which is in line with the experimental observation that daunomycin is protonated under physiological conditions. The intercalation interaction of protonated daunomycin with two stacked DNA base pairs was studied through a hybrid approach in which intercalation is treated at LDA/TZP while the molecular structure of daunomycin and hydrogen-bonded Watson-Crick pairs is c…

Metal Ions and Metal Complexes in Alzheimer's Disease.

Background: Alzheimer’s disease (AD) is the most common form of dementia that seriously affects daily life. Even if AD pathogenesis is still subject of debate, it is generally accepted that cerebral cortex plaques formed by aggregated amyloid-β (Aβ) peptides can be considered a characteristic pathological hallmark. It is well known that metal ions play an important role in the aggregation process of Aβ. Methods: This review focuses on the anti-Aβ aggregation activity of chelating ligands as well as on the use of metal complexes as diagnostic probes and as potential drugs. Conclusion: While chelating agents, such as curcumin or flavonoid derivatives, are currently used to capture metal ions …

Kinetic evidence for interaction of TMPyP4 with two different G-quadruplex conformations of human telomeric DNA

Background: Stabilization of G-quadruplex helices by small ligands has attracted growing attention because they inhibit the activity of the enzyme telomerase, which is overexpressed in> 80% cancer cells. TMPyP4, one of the most studied G-quadruplex ligands, is used as a model to show that the ligands can exhibit different binding features with different conformations of a human telomeric specific sequence. Methods: UV–Vis, FRET melting Assay, Isothermal Titration Calorimetry, Time-resolved Fluorescence lifetime, T-Jump and Molecular Dynamics. Results: TMPyP4 yields two different complexes with two Tel22 telomeric conformations in the presence of Na+ or K+. T-Jump kinetic experiments show th…

Synthesis, spectroscopic characterization and in vitro antimicrobial activity of diorganotin(IV) dichloride adducts with [1,2,4]triazolo-[1,5-a]pyrimidine and 5,7-dimethyl-[1,2,4]triazolo-[1,5-a]pyrimidine

Abstract The heterocyclic ligands [1,2,4]triazolo-[1,5-a]pyrimidine (tp) and 5,7-dimethyl-[1,2,4]triazolo-[1,5-a]pyrimidine (dmtp), react with diorganotin dichlorides giving the addition compounds Me2SnCl2(tp)2, Et2SnCl2(tp)2, Me2SnCl2(dmtp)2, Et2SnCl2(dmtp)2, Bu2SnCl2(dmtp), Ph2SnCl2(dmtp). The organotin:ligand stoichiometry goes from 1:2 to 1:1 by increasing the steric hindrance of the organic groups bound to tin. The compounds have been characterized by means of infrared, 119Sn Mossbauer and 1H AND 13C NMR spectroscopy. The ligands presumably coordinate to tin classically through the nitrogen atom at the position 3. The 1:1 complexes adopt trigonal bipyramidal structures, with the organi…

Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages

AbstractDNA integrity is an important factor to assure genome stability and, more generally, cells and organisms’ viability. In presence of DNA damage, the normal cell cycle is perturbed while cells activate their repair processes. Although efficient, the repair system is not always able to ensure the complete restoration of gene integrity. In these cases, not only mutations may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold which induces apoptosis and the programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiations are the most toxic, due to their inherently difficult repair, which may lead to …

The molecular structure of N-hydroxyurea

Ab initio calculations were performed on the tautomers and conformers of N-hydroxyurea using a 6-31G** basis set. The minimum-energy structures have been found and the importance of the intramolecular hydrogen bond as the stabilizing factor was pointed out. © 1996 John Wiley & Sons, Inc.

DNA binding and biological activity of Cu(II) and Zn(II) complexes of a 2,5-diphenyl[1,3,4]oxadiazole macrocycle ligand.

On the G‐Quadruplex Binding of a New Class of Nickel(II), Copper(II), and Zinc(II) Salphen‐Like Complexes

Halloysite nanotubes-carbon dots hybrids multifunctional nanocarrier with positive cell target ability as a potential non-viral vector for oral gene therapy

Abstract Hypothesis The use of non-viral vectors for gene therapy is hindered by their lower transfection efficiency and their lacking of self-track ability. Experiments This study aims to investigate the biological properties of halloysite nanotubes-carbon dots hybrid and its potential use as non-viral vector for oral gene therapy. The morphology and the chemical composition of the halloysite hybrid were investigated by means of high angle annular dark field scanning TEM and electron energy loss spectroscopy techniques, respectively. The cytotoxicity and the antioxidant activity were investigated by standard methods (MTS, DPPH and H2O2, respectively) using human cervical cancer HeLa cells …

CASSCF/CASPT2 analysis of the fragmentation of H2 on a Pd4 cluster

Two reactive pathways are described for the dissociative adsorption of a hydrogen molecule on a Pd4 pyramidal cluster, by using DFT/B3LYP and CASSCF/CASPT2 computational methods. Because of the different spin multiplicities of the cluster in the initial and final states, the reaction proceeds through a spin multiplicity change, which occurs close to the transition states. The activation energy values are very similar when the DFT method is used, whereas the CASPT2 calculations predict that the concerted mechanism is disfavored.

Toward a Rationale for the PTC124 (Ataluren) Promoted Readthrough of Premature Stop Codons: A Computational Approach and GFP-Reporter Cell-Based Assay

The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination c…

DNA-Binding of NiII, CuII and ZnII Complexes of Salen Derivatives

Nickel(II), copper(II) and zinc(II) complexes of N2O2 tetradentate Schiff base ligands strongly interact with B-DNA, usually by groove-binding and/or by intercalation [1]. It has been also shown that the presence of aromatic substituents on the N,N’ bridge make them suitable G-quadruplex binders [2]. In this context, we have recently investigated the binding toward duplex and G-quadruplex DNA of nickel(II), copper(II) and zinc(II) complexes of N,N’-bis-5-(triethyl ammonium methyl)-salicylidene-2,3-naphthalendiiminato) (see Figure), by spectroscopic and computational methods [3,4]. The compounds show also biological activity against human cancer cell lines. Different substituents are present…

Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses

Guanine quadruplexes (G4) structures in viral genome have a key role in modulating viruses’ biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modelling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.

G-quadruplex recognition by DARPIns through epitope/paratope analogy

AbstractWe investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments invo…

Design of copper(II) complexes as potential anticancer prodrugs

The fibroblast growth factor receptors (FGFR) are tyrosine kinases that are present in many types of endothelial and tumor cells and play an important role in cell growth, survival, and migration as well as in maintaining tumor angiogenesis (1). FGFR genetic alterations are frequently observed in cancer, suggesting that FGFR inhibition may be a promising therapy in patients harboring these lesions (2). In particular, molecules with structural properties similar to Ponatinib, a known inhibitor of FGFR, that shows a selective interaction for the ATP binding site of the isoform 4 of these receptors (FGFR4), are being considered. Molecular modeling studies have been conducted to design novel po…

A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex

The photophysical and DNA-binding properties of the cationic zinc(II) complex of 5-triethylammonium methyl salicylidene ortho-phenylenediiminato (ZnL 2 + ) were investi- gated by a combination of experimental and theoretical methods. DFT calculations were performed on both the ground and the first excited states of ZnL 2 + and on its possi- ble mono- and dioxidation products, both in vacuo and in selected solvents mimicked by the polarizable continuum model. Comparison of the calculated absorption and fluores- cence transitions with the corresponding experimental data led to the conclusion that visible light induces a two-elec- tron photooxidation process located on the phenylenediimi- nato…

A peptide from human β thymosin as a platform for the development of new anti-biofilm agents for Staphylococcus spp. and Pseudomonas aeruginosa

Conventional antibiotics might fail in the treatment of biofilm-associated infections causing infection recurrence and chronicity. The search for antimicrobial peptides has been performed with the aim to discover novel anti-infective agents active on pathogens in both planktonic and biofilm associated forms. The fragment 9-19 of human thymosin β4 was studied through 1 μs MD simulation. Two main conformations of the peptide were detected, both constituted by a central hydrophobic core and by the presence of peripheral charged residues suggesting a possible mechanism of interaction with two models of biological membranes, related to eukaryotic or bacterial membrane respectively. In addition, …

Photochemistry of 1,2,4-oxadiazoles. A DFT study on photoinduced competitive rearrangements of 3-amino- and 3-N-methylamino-5-perfluoroalkyl-1,2,4-oxadiazoles

The photoinduced competitive rearrangements of 5-perfluoroalkyl-3-amino(N-alkylamino)-1,2,4-oxadia- zoles have been investigated by DFT calculations and UV-vis spectroscopy. The observed product selectivity depends on the number of hydrogen atoms present in the amino moiety and involves two or three possible routes: (i) ring contraction-ring expansion (RCRE), (ii) internal-cyclization isomerization (ICI), or (iii) C(3)-N(2) migration-nucleophilic attack-cyclization (MNAC). UV absorption and fluorescence spectra of the reactants, and vertical excitation energy values, calculated by time dependent DFT, support the involvement of a neutral singlet excited state in the photoexcitation process. …

The Influence of the Amide Linkage in the FeIII-Binding Properties of Catechol-Modified Rosamine Derivatives

The two new fluorescent ligands RosCat1 and RosCat2 contain catechol receptors connected to rosamine platforms through an amide linkage and were synthesized by using microwave-assisted coupling reactions of carboxyl- or amine-substituted rosamines with the corresponding catechol units and subsequent deprotection. RosCat1 possesses a reverse amide, whereas RosCat2 has the usual oriented amide bond (HNCO vs. CONH, respectively). The ligands were characterized by means of NMR spectroscopy, mass-spectrometry, and DFT calculations and X-ray crystallography studies for RosCat1. The influence of the amide linkage on the photophysical properties of the fluorescent ligands was assessed in different …

Never Cared for What They Do: High Structural Stability of Guanine-Quadruplexes in the Presence of Strand-Break Damage

DNA integrity is an important factor that assures genome stability and, more generally, the viability of cells and organisms. In the presence of DNA damage, the normal cell cycle is perturbed when cells activate their repair processes. Although efficient, the repair system is not always able to ensure complete restoration of gene integrity. In these cases, mutations not only may occur, but the accumulation of lesions can either lead to carcinogenesis or reach a threshold that induces apoptosis and programmed cell death. Among the different types of DNA lesions, strand breaks produced by ionizing radiation are the most toxic due to the inherent difficultly of repair, which may lead to genomi…

The interaction of DNA with metal complexes: computational investigations

Confined But-2-ene catalytic isomerization inside H-ZSM-5 models: A DFT study

The isomerization of cis-but-2-ene to trans-but-2-ene within a 22T H-ZSM-5 zeolite model, also in the presence of two adsorbed Pd atoms, has been studied by DFT calculations. The results obtained allow us to state that the cis/trans but-2-ene isomerization can easily proceed inside unsupported zeolite cavities. In this case, differently than in the gas phase reaction, the trans-but-2-ene is less stable than the cis-but-2-ene, when adsorbed on the zeolite inner surface. Excluding the adsorption-desorption steps, the isomerization process involves two intermediates and three transition states, whose energy content is always very low with respect to that of reagents and intermediate species. T…

N -Diphenylmethyl-2-propenamide: theoretical study of the structure and interaction with a DNA model system

Abstract N -diphenylmethyl-2-propenamide (NDP) was synthesised and characterised. Pharmacological in vitro tests pointed out that NDP had a cytotoxic activity on a human ovarian carcinoma comparable to that of doxorubicin. Hypothesising that this in vitro cytotoxic activity could be mainly due to intercalating interactions, between the drug and DNA fragments, ab initio calculations, at the Hartree–Fock (HF) level, were performed on the structure, and on the conformational properties of NDP, whereas its interaction with an (AC)(TG) dinucleotide triphosphate duplex (DD) was studied by the ONIOM method, at HF and PM3 level for NDP and DD, respectively. The supposed intercalation process with t…

Molecular basis of SARS-CoV-2 infection and rational design of potential antiviral agents: Modeling and simulation approaches

International audience; The emergence in late 2019 of the coronavirus SARS-CoV-2 has resulted in the breakthrough of the COVID-19 pandemic that is presently affecting a growing number of countries. The development of the pandemic has also prompted an unprecedented effort of the scientific community to understand the molecular bases of the virus infection and to propose rational drug design strategies able to alleviate the serious COVID-19 morbidity. In this context, a strong synergy between the structural biophysics and molecular modeling and simulation communities has emerged, resolving at the atomistic level the crucial protein apparatus of the virus and revealing the dynamic aspects of k…

Mössbauer Investigation on Organotin Polyester Amines Containing Ciprofloxacin.

Organoplatinum(II) Complexes Self-Assemble and Recognize AT-Rich Duplex DNA Sequences

The specific recognition of AT-rich DNA sequences opens up the door to promising diagnostic and/or therapeutic strategies against gene-related diseases. Here, we demonstrate that amphiphilic PtII complexes of the type [Pt(dmba)(N∧N)]NO3 (dmba = N,N-dimethylbenzylamine-κN, κC; N∧N = dpq (3), dppz (4), and dppn (5)) recognize AT-rich oligonucleotides over other types of DNA, RNA, and model proteins. The crystal structure of 4 shows the presence of significant π-stacking interactions and a distorted coordination sphere of the d8 PtII atom. Complex 5, containing the largest π-conjugated ligand, forms supramolecular assemblies at high concentrations under aqueous environment. However, its aggreg…

Hydrogenation of 2,4-Dinitro-toluene on Pd/C Catalysts: Computational Study on the Influence of the Molecular Adsorption Modes and of Steric Hindrance and Metal Dispersion on the Reaction Mechanism

Abstract A new time-dependent Monte Carlo algorithm was developed to simulate isobar and isotherm three-phase batch hydrogenation of 2,4-dinitro-toluene on Pd/C catalysts. A new reaction mechanism was formulated, involving 9 and 27 toluene derivatives, in solution and adsorbed on the surface, respectively. In fact, three different ways of adsorption were considered for all surface derivatives. Microscopic mechanistic hypotheses were formulated analyzing the mimicked surface populations able to reproduce the experimental catalytic activity–selectivity patterns at different times, temperatures, reagent concentrations, and catalyst particle morphologies. The three different adsorption modes, g…

How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency.

AbstractThe STimulator of INterferon Genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP upon the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines which are crucial for protecting cells from infections. STING signaling pathway can also influence both tumor-suppressive and tumor-promoting mechanisms, rendering it an appealing target for drug design. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the differential molecular mechanisms exhibited by these variants is o…

Synthesis, characterization, and cellular investigations of porphyrin– and chlorin–indomethacin conjugates for photodynamic therapy of cancer

Indomethacin is a potent non-steroidal anti-inflammatory drug (NSAID) with a strong selective inhibitor activity towards cyclooxygenase-2 (COX-2), an enzyme that is highly overexpressed in various tumour cells, being involved in tumourigenesis. Concomitantly, porphyrins have gained much attention as promising photosensitizers (PSs) for the non-invasive photodynamic therapy (PDT) of cancer. Herein, we report the design, and determine the singlet oxygen generation capacity and in vitro cellular toxicity of porphyrin- and chlorin-indomethacin conjugates (P2-Ind and C2-Ind). Both the conjugates were obtained in high yields and were characterized by 1H, 19F and 13C NMR as well as by high resolut…

ChemInform Abstract: 1,2,3-Triazole in Heterocyclic Compounds, Endowed with Biological Activity, Through 1,3-Dipolar Cycloadditions

1,3-Dipolar cycloaddition reactions can be considered a powerful synthetic tool in the building of heterocyclic rings, with applications in different fields. In this review we focus on the synthesis of biologically active compounds possessing the 1,2,3-triazole core through 1,3-dipolar cycloaddition reactions. The 1,2,3-triazole skeleton can be present as a single disubstituted ring, as a linker between two molecules, or embedded in a polyheterocycle. The cycloaddition reactions are usually catalysed by copper or ruthenium. Domino reactions can be achieved through dipolarophile anion formation, generally followed by cyclisation. The variety of attainable heterocyclic structures gives an ill…

The interaction of deoxyribonucleic acid with methyltin(IV) moieties in solution studied by small-angle X-ray scattering, circular dichroism and UV spectroscopy

The nature of calf thymus DNA in aqueous solution, in the presence of the organotin(IV) species Sn IV Me 3 , Sn IV Me 2 and Sn IV Me, possibly partly hydrolysed and/or hydrated, was investigated by small-angle X-ray scattering (SAXS), ultraviolet spectroscopy (UV) at different temperatures and circular dichroism (CD). The results are compared with those of previous 119 Sn Mossbauer studies on condensed DNA phases. The effects of tin-phosphate oxygen bonding on the DNA melting profile in DNA-Sn IV Me systems are in agreement with previous reports on DNA-Main Group metal ion interactions. The structure and conformation of the DNA double helix are not influenced by Sn IV Me n species, even in …

The influence of substitution in the quinoxaline nucleus on 1,3-dipolar cycloaddition reactions

The reaction mechanism of 1,3-dipolar cycloadditions of both symmetric and unsymmetric benzo-condensed diazines with a nitrilimine dipole, to give two different mono- and bis-cycloadducts, in tetrahydrofuran (THF) solution, was studied by DFT calculatio ns. The results obtained show that each 1,3-dipolar cycloaddition reaction always proceeds by a two steps mechanism, in which the first intermediate shows only one covalent bond between the beta carbon of the nitrilimine and the aromatic nitrogen of the diazine molecule. The structure and energy content of the two transition states of the two cycloaddition steps, in the case of the unsymmetric benzo-condensed diazine, nicely explains why the…

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