The Da Vinci European BioBank: A Metabolomics-Driven Infrastructure.

We present here the organization of the recently-constituted da Vinci European BioBank (daVEB, https://www.davincieuropeanbiobank.org/it). The biobank was created as an infrastructure to support the activities of the Fiorgen Foundation (http://www.fiorgen.net/), a nonprofit organization that promotes research in the field of pharmacogenomics and personalized medicine. The way operating procedures concerning samples and data have been developed at daVEB largely stems from the strong metabolomics connotation of Fiorgen and from the involvement of the scientific collaborators of the foundation in international/European projects aimed to tackle the standardization of pre-analytical procedures and the promotion of data standards in metabolomics.

Protein aggregation starting from the native globular state.

Amyloid formation by globular proteins that normally adopt a compact folded structure is generally induced in vitro under harsh conditions involving low pH, high temperature, high pressure, or in the presence of organic solvents. Under these conditions, folded proteins are generally unfolded, at least partially. The approach described here shows a rationale and two detailed examples as to how the mechanism of aggregation of a globular protein can be probed under conditions in which it is initially in its folded conformation, and hence relevant to a physiological environment.

Amyloid formation from HypF-N under conditions in which the protein is initially in its native state.

Aggregation of the N-terminal domain of the Escherichia coli HypF (HypF-N) was investigated in mild denaturing conditions, generated by addition of 6-12% (v/v) trifluoroethanol (TFE). Atomic force microscopy indicates that under these conditions HypF-N converts into the same type of protofibrillar aggregates previously shown to be highly toxic to cultured cells. These convert subsequently, after some weeks, into well-defined fibrillar structures. The rate of protofibril formation, monitored by thioflavin T (ThT) fluorescence, depends strongly on the concentration of TFE. Prior to aggregation the protein has far-UV circular dichroism (CD) and intrinsic fluorescence spectra identical with those observed for the native protein in the absence of co-solvent; the quenching of the intrinsic tryptophan fluorescence by acrylamide and the ANS binding properties are also identical in the two cases. These findings indicate that HypF-N is capable of forming amyloid protofibrils and fibrils under conditions in which the protein is initially in a predominantly native-like conformation. The rate constants for folding and unfolding of HypF-N, determined in 10% TFE using the stopped-flow technique, indicate that a partially folded state is in rapid equilibrium with the native state and populated to ca 1%. A kinetic analysis reveals that aggregation results from molecules accessing such a partially folded state. The approach described here shows that it is possible to probe the mechanism of aggregation of a specific protein under conditions in which the protein is initially native and hence relevant to a physiological environment. In addition, the results indicate that toxic protofibrils can be formed from globular proteins under conditions that are only marginally destabilising and in which the large majority of molecules have the native fold. This conclusion emphasises the importance for cells to constantly combat the propensity for even the most stable of these proteins to aggregate.

Molecular recognition of metal complexes by DNA: a comparative study of the interactions of the parent complexes [PtCl(TERPY)]Cl and [AuCl(TERPY)]Cl2 with double stranded DNA.

The interactions of the parent complexes [AuCl(Terpy)]Cl(2) and [PtCl(Terpy)]Cl with DNA were analysed by various physicochemical methods. Surprisingly, these metal complexes produce different interaction patterns with DNA in spite of their profound structural similarity. Indeed, important modifications are detected in the characteristic UV-Vis bands of [PtCl(Terpy)]Cl upon addition of ct-DNA, while the spectrum of [AuCl(Terpy)]Cl(2) is almost unaffected. Gel electrophoresis studies confirm these findings: [PtCl(Terpy)]Cl - but not [AuCl(Terpy)]Cl(2) - retards significantly the mobility of the supercoiled form of the pHV14 plasmid after a short incubation time. Ultrafiltration studies indicate that the affinity of [PtCl(Terpy)]Cl for ct-DNA is significantly greater than that of [AuCl(Terpy)]Cl(2). On the other hand, both [AuCl(Terpy)]Cl(2) and [PtCl(Terpy)]Cl induce important changes in the CD spectrum of ct-DNA, at high concentration, and increase its T(m) value. Remarkably, the analysed metal-complex/DNA interaction patterns depend critically on the incubation times. We propose that [PtCl(Terpy)]Cl quickly intercalates DNA; then, formation of coordinative bonds progressively takes place with time. At variance, [AuCl(Terpy)]Cl(2) first interacts electrostatically with the DNA surface, with subsequent slow formation of some coordinative bonds.

Solution chemistry and cytotoxic properties of novel organogold(III) compounds.

The solution behaviour of some novel organogold(III) compounds was investigated, and their cytotoxic properties evaluated against a few human tumour cell lines (A2780/S, A2780/R, MCF7, HT29 and A549). Specifically, the following compounds were considered: [Au(bipy(dmb)-H)(2,6-xylidine-H)][PF(6)] (AuXyl) and [Au(bipy(dmb)-H)(p-toluidine-H)][PF(6)] (AuTol) (in which bipy(dmb)=6-(1,1-dimethylbenzyl)-2,2'-bipyridine), [Au(py(dmb)-H)(AcO)(2)] (AuPyAcO) (in which py(dmb)=2-(1,1-dimethylbenzyl)-pyridine) and [Au(pz(Ph)-H)Cl(3)]K (AuPzCl) (in which pz(Ph)=1-phenylpyrazole). The solution chemistry of these compounds, under physiological-like conditions, was investigated through UV-vis absorption and (1)H NMR spectroscopies. Significant cytotoxic effects in vitro were observed in selected cases.

Gold complexes inhibit mitochondrial thioredoxin reductase: consequences on mitochondrial functions.

The effects of gold(I) complexes (auranofin, triethylphosphine gold and aurothiomalate), gold(III) complexes ([Au(2,2'-diethylendiamine)Cl]Cl(2), [(Au(2-(1,1-dimethylbenzyl)-pyridine) (CH(3)COO)(2)], [Au(6-(1,1-dimethylbenzyl)-2,2'-bipyridine)(OH)](PF(6)), [Au(bipy(dmb)-H)(2,6-xylidine)](PF(6))), metal ions (zinc and cadmium acetate) and metal complexes (cisplatin, zinc pyrithione and tributyltin) on mitochondrial thioredoxin reductase and mitochondrial functions have been examined. Both gold(I) and gold(III) complexes are extremely efficient inhibitors of thioredoxin reductase showing IC(50) ranging from 0.020 to 1.42 microM while metal ions and complexes not containing gold are less effective, exhibiting IC(50) going from 11.8 to 76.0 microM. At variance with thioredoxin reductase, auranofin is completely ineffective in inhibiting glutathione peroxidase and glutathione reductase, while gold(III) compounds show some effect on glutathione peroxidase. The mitochondrial respiratory chain is scarcely affected by gold compounds while the other metal complexes and metal ions, in particular zinc ion and zinc pyrithione, show a more marked inhibitory effect that is reflected on a rapid induction of membrane potential decrease that precedes swelling. Therefore, differently from gold compounds, the various metal ions and metal complexes exert their effect on different targets indicating a lower specificity. It is concluded that gold compounds are highly specific inhibitors of mitochondrial thioredoxin reductase and this action influences other functions such as membrane permeability properties. Metal ions and metal complexes markedly inhibit the activity of thioredoxin reductase although to an extent lower than that of gold compounds. They also inhibit mitochondrial respiration, decrease membrane potential and, finally, induce swelling.

Reactions of gold(III) complexes with serum albumin.

The reactions of a few representative gold(III) complexes -[Au(ethylenediamine)2]Cl3, [Au(diethylentriamine)Cl]Cl2, [Au(1,4,8,11-tetraazacyclotetradecane)](ClO4)2Cl, [Au(2,2',2'-terpyridine)Cl]Cl2, [Au(2,2'-bipyridine)(OH)2][PF6] and the organometallic compound [Au(6-(1,1-dimethylbenzyl)-2,2'-bipyridine-H)(OH)][PF6]- with BSA were investigated by the joint use of various spectroscopic methods and separation techniques. Weak metal-protein interactions were revealed for the [Au(ethylenediamine)2]3+ and [Au(1,4,8,11-tetraazacyclotetradecane)]3+ species, whereas progressive reduction of the gold(III) centre was observed in the cases of [Au(2,2'-bipyridine)(OH)2]+ and [Au(2,2',2'-terpyridine)Cl]2+. In contrast, tight metal-protein adducts are formed when BSA is reacted with either [Au(diethylentriamine)Cl]2+ and [Au(6-(1,1-dimethylbenzyl)-2,2'-bipyridine-H)(OH)]+. Notably, binding of the latter complex to serum albumin results in the appearance of characteristic CD bands in the visible spectrum. It is suggested that adduct formation for both of these gold(III) complexes occurs through coordination at the level of surface histidines. Stability of these gold(III) complexes/serum albumin adducts was tested under physiologically relevant conditions and found to be appreciable. Metal binding to the protein is tight; complete detachment of the metal from the protein has been achieved only after the addition of excess potassium cyanide. The implications of the present results for the pharmacological activity of these novel cytotoxic agents are discussed.

Study of ruthenium(II) complexes with anticancer drugs as ligands. Design of metal-based phototherapeutic agents.

The reaction of trans-[RuCl(2)(PPh(3))(3)] (Ph = C(6)H(5)) with 2-thio-1,3-pyrimidine (HTPYM) and 6-thiopurines (TPs) produced mainly crystalline solids that consist of cis,cis,trans-[Ru(PPh(3))(2)(N,S-TPYM)(2)] (1) and cis,cis,trans-[Ru(PPh(3))(2)(N(7),S-TPs)(2)]X(2) (X = Cl(-), CF(3)SO(3)(-)). In the case of TPs, other coordination isomers have never been isolated and reported. Instead, the mother liquor obtained after filtration of 1 produced red single crystals of trans,cis,cis-[Ru(PPh(3))(2)(N,S-TPYM)(2)].2H(3)O(+).2Cl(-) (2.2H(3)O(+).2Cl(-)). Selected ruthenium(II)-thiobase complexes were studied for their structural, reactivity, spectroscopic, redox, and cytotoxic properties. Single crystals of 1 contain thiopyrimidinato anions chelated to the metal center via N and S. The Ru[bond]N bonds are significantly elongated for 1 [2.122(2) and 2.167(2) A] with respect to 2 [2.063(3) A] because of the trans influence from PPh(3). The coordination pseudo-octahedron for 2 is significantly elongated at the apical sites (PPh(3) ligands). Solutions of cis,cis,trans isomers in air are stable for weeks, whereas those of 2 turn green within 24 h, in agreement with the respective redox potentials. cis,cis,trans- and trans,cis,cis-[Ru(PH(3))(2)(N,S-TPYM)(2)], as optimized through the DFT methods at the Becke3LYP level are in good agreement with experimental geometrical parameters (1 and 2), with cis,cis,trans being more stable than trans,cis,cis by 3.88 kcal. The trend is confirmed by molecular modeling based on semiempirical (ZINDO/1) and molecular mechanics (MM) methods. Cytotoxic activity measurements for cis,cis,trans-[Ru(PPh(3))(N-THZ)(N(7),S -H(2)TP)(2)]Cl(2) (4) (THZ = thiazole, H(2)TP = 6-thiopurine) and cis,cis,trans-[Ru(PPh(3))(2)(N(7),S-HTPR)2]Cl(2) (5) (HTPR = 6-thiopurine riboside) against ovarian cancer cells A2780/S gave IC(50) values of 17 +/- 1 and 29 +/- 9 microM, respectively. Furthermore, the spectral analysis of HTPYM, TPs, and their Ru(II) complexes in solution shows that intense absorptions occur in the UVA/vis region of light, whereas standard nucleobases absorb in the UVB region.

Modeling of copper(II) sites in proteins based on histidyl and glycyl residues.

The complexes between copper(II) and four synthetic tetrapeptides bearing a single histidine residue within the sequence (AcHGGG, AcGHGG, AcGGHG and AcGGGH, respectively), have been investigated by potentiometric and spectroscopic methods (UV-Vis, circular dichroism and electron paramagnetic resonance). Potentiometric studies in the pH range 4-12 allowed identification and quantitative determination of the species present in solution for each copper-peptide complex. In all cases, upon raising pH, copper(II) coordination starts from the imidazole nitrogen of the His; afterwards three deprotonated amide nitrogens are progressively involved in copper coordination, except in the case of AcGHGG. Based on the potentiometric and spectroscopic results, detailed molecular structures are proposed for the dominant copper(II) tetrapeptide species existing in solution, either at neutral or alkaline pH. The structural consequences of the presence and of the location of a unique histidine residue within the tetrameric sequence are specifically analyzed. Results are discussed in relation to the modeling of copper(II) binding sites in proteins, particular emphasis being devoted to the copper complexes of the prion protein.

Structural features of a new dinuclear platinum(II) complex with significant antiproliferative activity.

A novel dinuclear platinum(II) complex, [Pt(2)-N,N'-bis(2-dimethylaminoethyl oxamide)Cl(4)], showing peculiar structural features, has been prepared and characterized. X-ray diffraction data reveal that the two platinum ions are simultaneously bound to the N,N'-bis(2-dimethylaminoethyl) oxamide ligand, on opposite sides. The coordination environment of both platinum centers is square planar, with identical NOCl(2) donor sets. The complex is poorly soluble within a physiological buffer but moderately soluble in DMSO. Preliminary in vitro studies point out that this dinuclear platinum complex exhibits significant growth-inhibiting properties on a panel of cultured human tumor cell lines, although less pronounced than those of cisplatin.

Molecular structure, solution chemistry and biological properties of the novel [ImH][trans-IrCl(4)(Im)(DMSO)], (I) and of the orange form of [(DMSO)(2)H][trans-IrCl(4)(DMSO)(2)], (II), complexes.

The new iridium(III) complex, imidazolium[trans(DMSO,imidazole)tetrachloroiridate(III)], (I) (DMSO=dimethyl sulfoxide), and the orange form of [(DMSO)(2)H][trans(DMSO)(2)tetrachloroiridate(III)], (II) have been prepared and characterized, both in the solid state and in solution, by X-ray diffraction and by various physicochemical techniques. Single crystal X-ray diffraction studies point out that complex (II) is isomorphous to the ruthenium(III) analogue, [(DMSO)(2)H][trans-RuCl(4)(DMSO)(2)], (III). Crystallographic data are the following: a=16.028(2) A, b=24.699(3) A, c=8.262(1) A, in space group Pbca (Z=8) for (imidazolium)[trans(DMSO,imidazole)tetrachloroiridate(III)], (I); and a=9.189(2) A, b=16.511(4) A, c=14.028(3) A, beta=100.82(2) degrees in space group P2/n (Z=4) for [(DMSO)(2)H][trans(DMSO)(2)tetrachloroiridate(III)], (II). Visible absorption spectra show that both complexes are stable for several days, at pH 7.4, at room temperature. No significant chloride hydrolysis is observed, even at high temperature (70 degrees C), over 24 h. The extreme stability of these iridium(III) complexes within a physiological buffer was further assessed by (1)H NMR; in addition, cyclic voltammetry measurements evidenced a high stability of the oxidation state +3. Preliminary biological studies show that both complexes do not bind appreciably bovine serum albumin nor inhibit significantly the proliferation of representative human tumor cell lines, suggesting that hydrolysis of coordinated chlorides is a crucial feature for the biological properties and the antitumor activity of the parent ruthenium(III) complexes.

Gold(III) compounds as new family of anticancer drugs.

Gold(III) complexes are emerging as a new class of metal complexes with outstanding cytotoxic properties and are presently being evaluated as potential antitumor agents. This renewed interest is the result of recent studies in which various gold(III) complexes have been shown to be stable under physiological conditions and to manifest relevant antiproliferative properties against selected human tumor cell lines. The pharmacological investigation of some representative gold(III) complexes has been extended to consider their effects on the cell cycle and to reveal induction of apoptosis. Remarkably, preliminary studies suggest that the interactions in vitro of gold(Ill) complexes with calf thymus DNA are weak whereas significant binding to model proteins takes place. Our findings imply that the mechanism of action of cytotoxic gold(Ill) complexes might be substantially different from that of clinically established platinum compounds.

Au2trien: a dinuclear gold(III) complex with unprecedented structura features.

The X-ray structure of a dinuclear gold(III) complex, Au2trien, shows the presence of two square planar gold(III) centers bridged by a nitrogen donor, in a very unusual fashion.

Gold(III) complexes as a new family of cytotoxic and antitumor agents.

In recent years, owing to the contributions of a few research groups, some new gold(III) compounds--either simple coordination complexes or organogold compounds--have been prepared that are sufficiently stable under physiological conditions and are promising candidates for pharmacological testing as cytotoxic and antitumor agents. In vitro pharmacological studies point out that some of these novel gold(III) complexes are highly cytotoxic toward cultured human tumor cell lines and are able to overcome resistance to platinum. Significant differences in the spectrum of action were observed compared with cisplatin. Studies are in progress to elucidate the mechanism of action of these compounds. The cellular effects of two representative gold(III) complexes are described. Preliminary results on binding to DNA in vitro are presented, pointing out that the interactions are generally weak. The implications of these results for the development of gold(III) complexes as a new family of cytotoxic and antitumor agents are discussed.

Gold(III) complexes with bipyridyl ligands: solution chemistry, cytotoxicity, and DNA binding properties.

Gold(III) compounds generally exhibit significant cytotoxic effects on cancer cell lines and are of potential interest as antitumor drugs. We report here on the solution chemistry, the cytotoxicity, and the DNA binding properties of two new bipyridyl gold(III) compounds: [Au(bipy)(OH)(2)][PF(6)] (1) and the organometallic compound [Au(bipy(c)-H)(OH)][PF(6)] (2) (bipy(c) = 6-(1,1-dimethylbenzyl)-2,2'-bipyridine). Both compounds are sufficiently soluble, and stable for hours, within a physiological buffer at 37 degrees C; [Au(bipy)(OH)(2)][PF(6)], at variance with [Au(bipy(c)-H)(OH)][PF(6)], is quickly and quantitatively reduced by ascorbate. Both compounds showed relevant cytotoxic effects toward the A2780S, A2780R, and SKOV3 tumor cell lines; lower effects were detected on the CCRF-CEM/S and CCRF-CEM/R lines. In most cases the mechanisms of resistance to CDDP are only marginally effective against these gold(III) complexes. The interactions of [Au(bipy)(OH)(2)][PF(6)] and [Au(bipy(c)-H)(OH)][PF(6)] with calf thymus DNA were investigated in vitro by various techniques to establish whether DNA represents a primary target for these compounds. Addition of saturating amounts of DNA did not affect appreciably the visible spectra of these gold(III) complexes. Some slight modifications of the CD spectra of calf thymus DNA and of the DNA melting parameters were observed; in any case, ultrafiltration experiments showed that binding of these gold(III) complexes to DNA is weak and reversible. The mechanistic implications of these findings are discussed.