Intrinsic fluorescence of the clinically approved multikinase inhibitor nintedanib reveals lysosomal sequestration as resistance mechanism in FGFR-driven lung cancer

Background Studying the intracellular distribution of pharmacological agents, including anticancer compounds, is of central importance in biomedical research. It constitutes a prerequisite for a better understanding of the molecular mechanisms underlying drug action and resistance development. Hyperactivated fibroblast growth factor receptors (FGFRs) constitute a promising therapy target in several types of malignancies including lung cancer. The clinically approved small-molecule FGFR inhibitor nintedanib exerts strong cytotoxicity in FGFR-driven lung cancer cells. However, subcellular pharmacokinetics of this compound and its impact on therapeutic efficacy remain obscure. Methods 3-dimens…

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…

Cover Picture: Complexation and Extraction of PAHs to the Aqueous Phase with a Dinuclear Pt II Diazapyrenium‐Based Metallacycle (Chem. Eur. J. 41/2010)

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.

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…

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…

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 …

Complexation and extraction of pyrene to the aqueous phase using a Pt(II) diazapyrenium-based metallocycle

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…

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…

Rapid generation of hydrogen peroxide contributes to the complex cell death induction by the angucycline antibiotic landomycin E

Landomycin E (LE) is an angucycline antibiotic produced by Streptomyces globisporus. Previously, we have shown a broad anticancer activity of LE which is, in contrast to the structurally related and clinically used anthracycline doxorubicin (Dx), only mildly affected by multidrug resistance-mediated drug efflux. In the present study, cellular and molecular mechanisms underlying the anticancer activity of landomycin E towards Jurkat T-cell leukemia cells were dissected focusing on the involvement of radical oxygen species (ROS). LE-induced apoptosis distinctly differed in several aspects from the one induced by Dx. Rapid generation of both extracellular and cell-derived hydrogen peroxide alr…

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 …

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…

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

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

Subcellular duplex DNA and G‐quadruplex interaction profiling of a hexagonal PtII metallacycle

[Abstract] Metal‐driven self‐assembly afforded a multitude of fascinating supramolecular coordination complexes (SCCs) with applications as catalysts, host–guest, and stimuli‐responsive systems. However, the interest in the biological applications of SCCs is only starting to emerge and thorough characterization of their behavior in biological milieus is still lacking. Herein, we report on the synthesis and detailed in‐cell tracking of a Pt2L2 metallacycle. We show that our hexagonal supramolecule accumulates in cancer cell nuclei, exerting a distinctive blue fluorescence staining of chromatin resistant to UV photobleaching selectively in nucleolar G4‐rich regions. SCC co‐localizes with epit…

Complexation and Extraction of PAHs to the Aqueous Phase with a Dinuclear Pt II Diazapyrenium‐Based Metallacycle

New palladium and platinum metallacycles have been synthesized by reaction between a 2,7-diazapyrenium-based ligand and Pd(II) and Pt(II) complexes. The inclusion complexes between the metallacycles and polycyclic aromatic hydrocarbons (PAHs) in CD(3)NO(2) and D(2)O were studied by NMR spectroscopy. The structures of the inclusion complexes of the Pt metallacycle as host with pyrene, phenanthrene, and triphenylene were confirmed by single crystal X-ray crystallography. The association constants between the Pt metallacycle and the selected PAHs were determined in CH(3)CN following the characteristic charge-transfer band displayed in their UV/Vis absorption spectrum. Although in aqueous solut…

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.

Fluorescent organometallic rhodium(I) and ruthenium(II) metallodrugs with 4-ethylthio-1,8-naphthalimide ligands: Antiproliferative effects, cellular uptake and DNA-interaction

Fluorescent 4-ethylthio-1,8-naphthalimides containing rhodium(I) N-heterocyclic carbene (NHC) and ruthenium (II) NHC fragments were synthesised and evaluated for their antiproliferative effects, cellular uptake and DNA-binding activity. Both types of organometallics triggered ligand dependent efficient cytotoxic effects against tumor cells with the rhodium(I) NHC derivatives causing stronger effects than the ruthenium (II) NHC analogues. Antiproliferative effects could also be observed against several pathogenic Gram-positive bacterial strains, whereas the growth of Gram-negative bacteria was not substantially affected. Cellular uptake was confirmed by atomic absorption spectroscopy as well…

Landomycins as glutathione-depleting agents and natural fluorescent probes for cellular Michael adduct-dependent quinone metabolism

Landomycins are angucyclines with promising antineoplastic activity produced by Streptomyces bacteria. The aglycone landomycinone is the distinctive core, while the oligosaccharide chain differs within derivatives. Herein, we report that landomycins spontaneously form Michael adducts with biothiols, including reduced cysteine and glutathione, both cell-free or intracellularly involving the benz[a]anthraquinone moiety of landomycinone. While landomycins generally do not display emissive properties, the respective Michael adducts exerted intense blue fluorescence in a glycosidic chain-dependent manner. This allowed label-free tracking of the short-lived nature of the mono-SH-adduct followed b…

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…

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…

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 …

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

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…

Synthesis and Biological Evaluation of Organometallic Complexes Bearing Bis‐1,8‐naphthalimide Ligands

Organometallic N-heterocyclic carbene (NHC) complexes with intercalating bis-naphthalimide ligands were prepared and evaluated biologically. Cytotoxic effects against tumor cells or bacteria were strongly ligand dependent with minor influence of the metal (Ag, Ru, Rh, Au) centers. Complex 8b with a rhodium(I) NHC moiety was studied in more detail for its DNA interacting properties in comparison to the metal free ligand. These studies showed a good DNA binding pattern with some preference for the telomeric quadruplex structure hTelo. Complex 8b was also shown to trigger additional coordinative binding to the DNA and therefore represents an useful tool compound with a mixed intercalative/coor…

Biological activity of PtIV prodrugs triggered by riboflavin-mediated bioorthogonal photocatalysis

AbstractWe have recently demonstrated that riboflavin (Rf) functions as unconventional bioorthogonal photocatalyst for the activation of PtIV prodrugs. In this study, we show how the combination of light and Rf with two PtIV prodrugs is a feasible strategy for light-mediated pancreatic cancer cell death induction. In Capan-1 cells, which have high tolerance against photodynamic therapy, Rf-mediated activation of the cisplatin and carboplatin prodrugs cis,cis,trans-[Pt(NH3)2(Cl)2(O2CCH2CH2CO2H)2] (1) and cis,cis,trans-[Pt(NH3)2(CBDCA)(O2CCH2CH2CO2H)2] (2, where CBDCA = cyclobutane dicarboxylate) resulted in pronounced reduction of the cell viability, including under hypoxia conditions. Such …

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.

Targeting a Targeted Drug: An Approach Toward Hypoxia-Activatable Tyrosine Kinase Inhibitor Prodrugs

Tyrosine kinase inhibitors (TKIs), which have revolutionized cancer therapy over the past 15 years, are limited in their clinical application due to serious side effects. Therefore, we converted two approved TKIs (sunitinib and erlotinib) into 2-nitroimidazole-based hypoxia-activatable prodrugs. Kinetics studies showed very different stabilities over 24 h; however, fast reductive activation via E. coli nitroreductase could be confirmed for both panels. The anticancer activity and signaling inhibition of the compounds against various human cancer cell lines were evaluated in cell culture. These data, together with molecular docking simulations, revealed distinct differences in the impact of …

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…

Metal drugs and the anticancer immune response

The immune system deploys a multitude of innate and adaptive mechanisms not only to ward off pathogens but also to prevent malignant transformation ("immune surveillance"). Hence, a clinically apparent tumor already reflects selection for those malignant cell clones capable of evading immune recognition ("immune evasion"). Metal drugs, besides their well-investigated cytotoxic anticancer effects, massively interact with the cancer-immune interface and can reverse important aspects of immune evasion. This topic has recently gained intense attention based on combination approaches with anticancer immunotherapy (e.g., immune checkpoint inhibitors), a strategy recently delivering first exciting…

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…

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…

Ruthenium-arene complexes bearing naphthyl-substituted 1,3-dioxoindan-2-carboxamides ligands for G-quadruplex DNA recognition.

Quadruplex nucleic acids – DNA/RNA secondary structures formed in guanine rich sequences – proved to have key roles in the biology of cancers and, as such, in recent years they emerged as promising targets for small molecules. Many reports demonstrated that metal complexes can effectively stabilize quadruplex structures, promoting telomerase inhibition, downregulation of the expression of cancer-related genes and ultimately cancer cell death. Although extensively explored as anticancer agents, studies on the ability of ruthenium arene complexes to interact with quadruplex nucleic acids are surprisingly almost unknown. Herein, we report on the synthesis and characterization of four novel Ru(…

Interplay of three G‑quadruplex units in the KIT promoter

The proto-oncogene KIT encodes for a tyrosine kinase receptor, which is a clinically validated target for treating gastrointestinal stromal tumors. The KIT promoter contains a G-rich domain within a relatively long sequence potentially able to form three adjacent G-quadruplex (G4) units, namely, K2, SP, and K1. These G4 domains have been studied mainly as single quadruplex units derived from short truncated sequences and are currently considered promising targets for anticancer drugs, alternatively to the encoded protein. Nevertheless, the information reported so far does not contemplate the interplay between those neighboring G4s in the context of the whole promoter, possibly thwarting dru…

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

Self-Ordering Secondary Structure of d- and l-Arginine-Derived Polyamidoamino Acids

This paper reports on synthesis, acid–base properties and pH-dependent structuring in water of d-, l- and d,l-ARGO7, bioinspired polymers obtained by polyaddition of the corresponding arginine stereoisomers with N,N′-methylenebis(acrylamide). The circular dichroism spectra of d- and l-ARGO7 showed a peak at 228 nm and quickly and reversibly responded to pH changes, but were nearly unaffected by temperature, ionic strength, and denaturating agents. Theoretical modeling studies of L-ARGO7 showed that it assumed a folded structure. Intramolecular interactions led to transoid arrangements of the main chain reminiscent of the protein hairpin motif. Torsion angles showed a quite similar distribut…

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.

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

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 …

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…

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

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 …

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…

Development and biological investigations of hypoxia-sensitive prodrugs of the tyrosine kinase inhibitor crizotinib

Despite the huge success of tyrosine kinase inhibitors as anticancer agents, severe side effects are a major problem. In order to overcome this drawback, the first hypoxia-activatable 2-nitroimidazole-based prodrugs of the clinically approved ALK and c-MET inhibitor crizotinib were developed. The 2-aminopyridine functionality of crizotinib (essential for target kinase binding) was considered as ideal position for prodrug derivatization. Consequently, two different prodrugs were synthesized with the nitroimidazole unit attached to crizotinib either via carbamoylation (A) or alkylation (B) of the 2-aminopyridine moiety. The successful prodrug design could be proven by docking studies and a dr…

[2]Catenanes and inclusion complexes derived from self-assembled rectangular PdII and PtII metallocycles

New inclusion complexes and [2]catenanes were self-assembled from a fluorescent diazapyrenium based ligand, a PdII or PtII complex, and cyclic or acyclic electron rich aromatic guests in aqueous and organic media. The molecular rectangles display a π-deficient cavity suitable to incorporate π-donor aromatic systems. The inclusion complexes between the metallocycles and phenylenic (2a,b) and naphthalenic (3a,b–5a,b) derivatives were studied by NMR, UV-vis and fluorescence spectroscopy. The crystal structure of (3b) ⊂ 1a·6PF(6) confirmed the insertion of the guest into the cavity of the metallocycle. Following the same self-assembly strategy, the use of polyethers 6,7 as π-donors resulted in …

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…

Anticancer metal drugs and immunogenic cell death

Conventional chemotherapeutics, but also innovative precision anticancer compounds, are commonly perceived to target primarily the cancer cell compartment. However, recently it was discovered that some of these compounds can also exert immunomodulatory activities which might be exploited to synergistically enhance their anticancer effects. One specific phenomenon of the interplay between chemotherapy and the anticancer immune response is the so-called “immunogenic cell death” (ICD). ICD was discovered based on a vaccination effect exerted by cancer cells dying from pretreatment with certain chemotherapeutics, termed ICD inducers, in syngeneic transplantation mouse models. Interestingly, onl…

Self-assembled Pt2L2 boxes strongly bind G-quadruplex DNA and influence gene expression in cancer cells

Supramolecular Pt(ii) quadrangular boxes bind native and G-quadruplex DNA motifs in a size-dependent fashion. Three Pt molecular squares of distinct size show biological activity against cancer cells and heavily influence the expression of genes known to form G-quadruplexes in their promoter regions. The smallest Pt-box displays less activity but more selectivity for a quadruplex formed in the c-Kit gene.

Synthesis, antiproliferative activity, and in silico insights of new 3-benzoylamino-benzo[ b ]thiophene derivatives

A new series of 3-benzoylamino-5-imidazol-5-yl-benzo[b]thiophenes and the parent amino derivatives were synthesized and screened as antitumor agents. All tested compounds showed concentration-dependent antiproliferative activity profile against HeLa cell line, exhibiting GI50 values in the low micromolar range. The most active compounds were tested in cell cycle perturbation experiments. A rapid accumulation of cells in the G2/M phase, with a concomitant reduction of cells in both the S and G0/G1 phases, was observed, suggesting that cell exposure to selected derivatives produces mitotic failure. To rationalize the biological results, the 3-benzoylamino-benzo[b]thiophenes were analyzed thro…

Anticancer platinum agents and light

Abstract Since the discovery of cisplatin, light activation has been employed as a strategy to switch and improve the anticancer effects of platinum compounds. This contribution highlights some of the most representative discoveries obtained in the field of platinum-based photochemotherapy over the years.

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…

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…

DNA Binding and Biological Activity of Transition Metal Complexes

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

Near-infrared photochemistry assisted by upconverting nanoparticles

Abstract Upconverting nanoparticles (UCNPs) combine unique optical and imaging properties with high chemical and biological stability. The capability of UCNPs to emit visible light upon near-infrared light excitation, in an anti-Stokes fashion, is extremely attractive for the design of light-responsive nanomaterials whose action can be controlled spatially and temporally. In this chapter, we analyze the most promising approaches developed so far to functionalize the surface of UCNPs with photoactivatable organic and inorganic molecular systems. In particular, we emphasize the key advances in the design of upconverting nanosystems that exploit bioactive transition metal complexes.

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…

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…

Metal complexes of oxadiazole ligands: An overview

Oxadizoles are heterocyclic ring systems that find application in different scientific disciplines, from medicinal chemistry to optoelectronics. Coordination with metals (especially the transition ones) proved to enhance the intrinsic characteristics of these organic ligands and many metal complexes of oxadiazoles showed attractive characteristics for different research fields. In this review, we provide a general overview on different metal complexes and polymers containing oxadiazole moieties, reporting the principal synthetic approaches adopted for their preparation and showing the variety of applications they found in the last 40 years.

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…

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…

124I Radiolabeling of a AuIII‐NHC Complex for In Vivo Biodistribution Studies†

Abstract AuIII complexes with N‐heterocyclic carbene (NHC) ligands have shown remarkable potential as anticancer agents, yet their fate in vivo has not been thoroughly examined and understood. Reported herein is the synthesis of new AuIII‐NHC complexes by direct oxidation with radioactive [124I]I2 as a valuable strategy to monitor the in vivo biodistribution of this class of compounds using positron emission tomography (PET). While in vitro analyses provide direct evidence for the importance of AuIII‐to‐AuI reduction to achieve full anticancer activity, in vivo studies reveal that a fraction of the AuIII‐NHC prodrug is not immediately reduced after administration but able to reach the major…

Influence of thermally induced structural transformations on the magnetic and luminescence properties of tartrate-based chiral lanthanide organic-frameworks

This work reports on the synthesis and characterization of five enantiomeric pairs of isostructural 3D metal-organic frameworks (MOFs) with the general formula {[Ln2(μ4-tar)2(μ-tar)(H2O)2]·xH2O}n [where Ln(iii) = Tb (Tb-L and Tb-D), Dy (Dy-L and Dy-D), Ho (Ho-L and Ho-D), Er (Er-L and Er-D) and Tm (Tm-L and Tm-D); tar = tartrate (d- or l-) and x = 3 or 4 depending on the counterpart], which possess interesting luminescence and magnetic properties. These MOFs undergo progressive and reversible dehydration processes upon controlled heating yielding three crystalline phases (Ln-L′, Ln-L′′ and Ln-L′′′). Alternating current magnetic measurements on Tb, Dy and Er-based compounds exhibit field ind…

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

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…

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…

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…

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…

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.

Transition Metal Complexes as DNA-intercalators

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 …

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 …

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

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.

Enantiospecific Response in Cross-Polarization Solid-State Nuclear Magnetic Resonance of Optically Active Metal Organic Frameworks.

We report herein on a NMR-based enantiospecific response for a family of optically active metal-organic frameworks. Cross-polarization of the 1H-13C couple was performed, and the intensities of the 13C nuclei NMR signals were measured to be different for the two enantiomers. In a direct-pulse experiment, which prevents cross-polarization, the intensity difference of the 13C NMR signals of the two nanostructured enantiomers vanished. This result is due to changes of the nuclear spin relaxation times due to the electron spin spatial asymmetry induced by chemical bond polarization involving a chiral center. These experiments put forward on firm ground that the chiral-induced spin selectivity e…

The interaction of transition metal complexes with deoxyribonucleic acid

La presente tesi `e suddivisa in quattro capitoli. Il Capitolo 1 `e di carattere introduttivo. Nel Capitolo 2 viene trattata la sintesi e la caratterizzazione strutturale dei complessi di CuII, NiII e ZnII con il legante N,N’-Bis-5-(trietil ammonio metil salicilidene)-1,2- fenilendiammina. Inoltre, vengono riportati e confrontati i risultati dello studio della loro interazione con DNA nativo. Viene in particolare mostrato come l’interazione con DNA aumenti la stabilit`a fotochimica del complesso di ZnII. Infine, vengono evidenziati gli effetti del confinamento in cristalli liquidi sull’interazione del complesso di CuII e DNA.Nel Capitolo 3 `e riportata la sintesi e la caratterizzazione stru…

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…

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…

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

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…

Metal NHC Complexes with Naphthalimide Ligands as DNA-Interacting Antiproliferative Agents

Naphthalimide-based N-heterocyclic carbene (NHC) complexes of the type [(1,5-cyclooctadiene)(NHC)RhCl)] (4 a-c), [(p-cymene)(NHC)RuCl2 )] (5 a-c), and [(NHC)CuBr] (6 a-c) were synthesized and investigated as antiproliferative agents that target DNA. The cytotoxic effects were largely driven by the naphthalimide structure, which is a DNA-intercalating moiety. Regarding the metal center, the highest activities were observed with the rhodium complexes, and cytotoxic activity was significantly lower for the ruthenium derivatives. The stable coordination of the NHC ligands of selected complexes 4 b and 5 b in solution was confirmed, and their DNA binding properties were studied by UV/Vis spectro…

Catalysis Concepts in Medicinal Inorganic Chemistry

Catalysis has strongly emerged in the field of medicinal inorganic chemistry as a suitable tool to deliver new drug candidates and to overcome drawbacks associated to metallodrugs. In this Concept article, we discuss representative examples of how catalysis has been applied in combination with metal complexes to deliver new therapy approaches. In particular, we explain key achievements in the design of catalytic metallodrugs that damage biomolecular targets and in the development of metal catalysis schemes for the activation of exogenous organic prodrugs. Moreover, we discuss our recent discoveries on the flavin-mediated bioorthogonal catalytic activation of metal-based prodrugs; a new cata…

Amino acid-­deriving chiral polymers with potential for biotechnological applications

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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…

CCDC 1990183: Experimental Crystal Structure Determination

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CCDC 1989307: Experimental Crystal Structure Determination

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CCDC 1451695: Experimental Crystal Structure Determination

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CCDC 1981579: Experimental Crystal Structure Determination

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CCDC 1990182: Experimental Crystal Structure Determination

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CCDC 2058320: Experimental Crystal Structure Determination

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CCDC 1510249: Experimental Crystal Structure Determination

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CCDC 1870492: Experimental Crystal Structure Determination

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CCDC 1981582: Experimental Crystal Structure Determination

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CCDC 1451694: Experimental Crystal Structure Determination

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CCDC 1981573: Experimental Crystal Structure Determination

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CCDC 1981583: Experimental Crystal Structure Determination

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CCDC 1981580: Experimental Crystal Structure Determination

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CCDC 1451696: Experimental Crystal Structure Determination

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