Salmonella enterica serovar Typhimurium growth is inhibited by the concomitant binding of Zn(II) and a pyrrolyl-hydroxamate to ZnuA, the soluble component of the ZnuABC transporter.

BACKGROUND: Under conditions of Zn(II) deficiency, the most relevant high affinity Zn(II) transport system synthesized by many Gram-negative bacteria is the ZnuABC transporter. ZnuABC is absent in eukaryotes and plays an important role in bacterial virulence. Consequently, ZnuA, the periplasmic component of the transporter, appeared as a good target candidate to find new compounds able to contrast bacterial growth by interfering with Zn(II) uptake. METHODS: Antibacterial activity assays on selected compounds from and in-house library against Salmonella enterica serovar Typhimurium ATCC14028 were performed. The X-ray structure of the complex formed by SeZnuA with an active compound was solved at 2.15Å resolution. RESULTS: Two di-aryl pyrrole hydroxamic acids differing in the position of a chloride ion, RDS50 ([1-[(4-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid]) and RDS51 (1-[(2-chlorophenyl)methyl]-4-phenyl-1H-pyrrol-3-hydroxamic acid) were able to inhibit Salmonella growth and its invasion ability of Caco-2 cells. The X-ray structure of SeZnuA containing RDS51 revealed its presence at the metal binding site concomitantly with Zn(II) which is coordinated by protein residues and the hydroxamate moiety of the compound. CONCLUSIONS: Two molecules interfering with ZnuA-mediated Zn(II) transport in Salmonella have been identified for the first time. The resolution of the SeZnuA-RDS51 X-ray structure revealed that RDS51 is tightly bound both to the protein and to Zn(II) thereby inhibiting its release. These features pave the way to the rational design of new Zn(II)-binding drugs against Salmonella. GENERAL SIGNIFICANCE: The data reported show that targeting the bacterial ZnuABC transporter can represent a good strategy to find new antibiotics against Gram-negative bacteria.

Inhibition of Leishmania infantum trypanothione reductase by diaryl sulfide derivatives.

The study presented here aimed at identifying a new class of compounds acting against Leishmania parasites, the causative agent of Leishmaniasis. For this purpose, the thioether derivatives of our in-house library have been evaluated in whole-cell screening assays in order to determine their in vitro activity against Leishmania protozoan. Among them, promising results have been achieved with compound RDS 777 (6-(sec-butoxy)-2-((3-chlorophenyl)thio)pyrimidin-4-amine) (IC50 = 29.43 µM), which is able to impair the mechanism of the parasite defence against the reactive oxygen species by inhibiting the trypanothione reductase (TR) with high efficiency (Ki 0.25 ± 0.18 µM). The X-ray structure of L. infantum TR in complex with RDS 777 disclosed the mechanism of action of this compound that binds to the catalytic site and engages in hydrogen bonds the residues more involved in the catalysis, namely Glu466', Cys57 and Cys52, thereby inhibiting the trypanothione binding and avoiding its reduction.

Hypoglycemic activity of curcumin synthetic analogues in alloxan-induced diabetic rats.

The currently available therapies for type 2 diabetes have been unable to achieve normoglycemic status in the majority of patients. The reason may be attributed to the limitations of the drug itself or its side effects. In an effort to develop potent and safe oral antidiabetic agents, we evaluated the in vitro and in vivo hypoglycemic effects of 10 synthetic polyphenolic curcumin analogues on alloxan-induced male diabetic albino rats. In vitro studies showed 7-bis(3,4-dimethoxyphenyl)hepta-1,6-diene-3,5-dione (4) to be the most potential hypoglycemic agent followed by 1,5-bis(4-hydroxy-3-methoxyphenyl)penta-1,4-dien-3-one (10). Structure activity relationship (SAR) of the tested compounds was elucidated and the results were interpreted in terms of in vitro hypoglycemic activities. Furthermore, oral glucose tolerance test (OGTT) with compounds 4, 10 and reference hypoglycemic drug glipizide showed that compound 4 and glipizide had relatively similar effects on the reduction of blood glucose levels within 2 h. Thus, compound 4 might be regarded as a potential hypoglycemic agent being able to reduce glucose concentration both in vitro and in vivo.

Identification of highly conserved residues involved in inhibition of HIV-1 RNase H function by Diketo acid derivatives.

HIV-1 reverse transcriptase (RT)-associated RNase H activity is an essential function in viral genome retrotranscription. RNase H is a promising drug target for which no inhibitor is available for therapy. Diketo acid (DKA) derivatives are active site Mg(2+)-binding inhibitors of both HIV-1 RNase H and integrase (IN) activities. To investigate the DKA binding site of RNase H and the mechanism of action, six couples of ester and acid DKAs, derived from 6-[1-(4-fluorophenyl)methyl-1H-pyrrol-2-yl)]-2,4-dioxo-5-hexenoic acid ethyl ester (RDS1643), were synthesized and tested on both RNase H and IN functions. Most of the ester derivatives showed selectivity for HIV-1 RNase H versus IN, while acids inhibited both functions. Molecular modeling and site-directed mutagenesis studies on the RNase H domain demonstrated different binding poses for ester and acid DKAs and proved that DKAs interact with residues (R448, N474, Q475, Y501, and R557) involved not in the catalytic motif but in highly conserved portions of the RNase H primer grip motif. The ester derivative RDS1759 selectively inhibited RNase H activity and viral replication in the low micromolar range, making contacts with residues Q475, N474, and Y501. Quantitative PCR studies and fluorescence-activated cell sorting (FACS) analyses showed that RDS1759 selectively inhibited reverse transcription in cell-based assays. Overall, we provide the first demonstration that RNase H inhibition by DKAs is due not only to their chelating properties but also to specific interactions with highly conserved amino acid residues in the RNase H domain, leading to effective targeting of HIV retrotranscription in cells and hence offering important insights for the rational design of RNase H inhibitors.

Effects of polyphenol compounds on influenza A virus replication and definition of their mechanism of action.

A set of polyphenol compounds was synthesized and assayed for their ability in inhibiting influenza A virus replication. A sub-set of them showed low toxicity. The best compounds within this sub-set were 4 and 6g, which inhibited the viral replication in a dose-dependent manner. The antiviral activity of these molecules was demonstrated to be caused by their interference with intracellular pathways exploited for viral replication: (1) MAP kinases controlling nuclear-cytoplasmic traffic of viral ribonucleoprotein complex; (2) redox-sensitive pathways, involved in maturation of viral hemagglutinin protein.

Negatively charged gold atoms in subnanometric particles: experimental evidence from an X-ray photoelectron spectroscopy study.

The results of an X-ray Photoelectron Spectroscopy study conducted on a series of gold nanoparticles recently reported by us, stabilized by monodentate, bidentate, tridentate and tetradentate thiolate calix[n]arene ligands, are presented here. By virtue of the different denticity of the ligands, the nuclearity of the resulting particles can be tuned down to the subnanometric range. From the present XPS results, a clear correlation among the experimental binding energy of single Au 4f peak components and the specific Au state of charge is proposed, where the smaller (i.e., nanometer) fraction of the series selectively shows negatively charged Au atoms. Our findings are relevant for the open discussion of a specific role played by negatively charged Au atoms in catalytic reactions, especially at low temperatures.

Preparation, reactivity and controlled release of SAMs of calix[4,6]arenes and calix[6]arene-based rotaxanes and pseudorotaxanes formed on polycrystalline Cu.

Specific and reversible binding of guest molecules from a solution to a surface pre-treated with host molecules is a recent and active field of research. Self-assembled monolayers may result from supramolecular interactions, adding distinct functionalities to the surface. In this frame, the first compared study is given here of the anchoring on the technologically relevant Cu surface of calix[4]arene receptors and calix[6]arene-based rotaxanes and pseudorotaxanes. These molecules, which belong to the most representative classes of compounds in supramolecular chemistry, have been chosen for their synthetic accessibility and versatility, which make them useful building blocks for the synthesis of new advanced supramolecular structures. Covalent functionalisation of calix[4,6]arenes on Cu was reached via a dip-coating procedure, optimizing the various synthetic aspects in order to obtain good coverages and copper passivation. Molecular adhesion has been demonstrated by the presence and relative quantitation of XPS signals from specific elements in the molecules. We have successfully tested the combination of different functionalities by producing a mixed film, prepared by ligand exchange of calix[4]arene with undecanethiol. The availability of the calix[4]arene cavity to reversibly host further species after anchoring on Cu has been demonstrated by a sequence of uptake and release cycles with pyridinium salts. Rotaxane and pseudorotaxane species, composed of a calix[6]arene wheel functionalized with N-phenylurea groups on the upper rim, and a viologen-containing axle, have been anchored on Cu via the SH-termination of the axle. XPS demonstrated the successful self-assembly of fully threaded rotaxanes and pseudorotaxanes from their solutions and the controlled release upon biasing of full rotaxanes and of the pseudorotaxane wheel.

Surface grafting and reactivity of calixarene-based receptors and pseudorotaxanes on Si(100).

The first report is given here on the anchoring on H-Si(100) of calix[4]arenes and calix[6]arene-based pseudorotaxanes, versatile building blocks for molecular devices. Covalent functionalization on Si was reached through a wet chemistry recipe, by making use of an extra-mild photochemical activation via visible light of C=C terminated anchoring arms. Our approach largely preserves the integrity of the molecular substrate, also allowing for a full monolayer of pseudorotaxane to be formed on Si(100). Molecular adhesion has been demonstrated by the presence and quantitation of XPS signals from specific elements in the molecules. AFM measurements performed on Si(100)/calix[4]arenes have revealed structures 2.3 nm high, consistent with the length of the molecule. The availability of the calix[4]arene cavity to host further species after anchoring on Si has been demonstrated by the successful complexation reaction with Cs(+) ions, resulting in a 1:1 calix/Cs(+) ratio, and with N-methyl pyridinium iodide. A pseudorotaxane species, composed of a calix[6]arene wheel derivatised with N-phenylureido groups on the upper rim and a viologen (4,4'-bipyridinium) containing axle, has been anchored on Si(100) via the C=C termination of the axle. We demonstrated the self-assembling of this pseudorotaxane covalently bound by use of XPS.

Selective assembling of calixarenes and pseudorotaxanes on Si(100) and polycrystalline copper.

We report the first compared study of the anchoring mode of calix[6]arene derivatives and pseudorotaxanes on Si(100) and polycrystalline Cu. Calixarenes have been chosen for their flexibility as linkers, being, i.a., efficient building blocks for the constructing of molecular devices based on pseudorotaxanes and rotaxanes. A covalent functionalization on Si or Cu surfaces requires the molecules to be differently modified: thiol (-SH) or C double bond C terminations are respectively suitable for Cu or H-Si(100). Anchoring on Cu was reached by dipping a clean substrate in a calix[6]arene-SH solution, while a wet-chemistry recipe was followed for Si(100), combined with an extra-mild photochemical activation via visible light. Molecular adhesion onto either surfaces has been demonstrated by the presence of XPS signals from specific elements in the molecules: calix[6]arene designed for H-Si were derivatized with NO2 groups on the upper rim of the calix, while the S atom was used as the molecular identifier on Cu. A further extension is represented by the anchoring reaction of rotaxanes on Si(100) and Cu surfaces. A pseudorotaxane species was first formed in solution by reacting a calix[6]arene "wheel," bearing three N-phenylureido groups on the upper rim, with viologen (4,4'-bipyridinium) containing axle. The resulting species has then been anchored on either Cu and Si via its distinct termination of the axle. This two-step reaction has produced a threaded pseudorotaxane covalently bound to either surfaces, as shown by XPS results. These species are ready to respond to external stimuli. We also cross-checked the two different anchoring groups for their reactivity on Cu and Si surfaces. No molecular uptake was observed when two solutions, containing calixarenes with the anchoring arms intended either for Si or Cu surfaces, were exchanged.

The effect of ligand denticity in size-selective synthesis of calix[n]arene-stabilized gold nanoparticles: a multitechnique approach.

A series of gold nanoparticles (AuNPs) stabilized by monodentate, bidentate, and tridentate thiolate calix[n]arene ligands 1-3 was prepared by using the Brust-Schiffrin two-phase direct synthesis and characterized with NMR spectroscopy, elemental analysis, transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS). The experimental data show that the particular multidentate structure of calix[n]arene derivatives 2 and 3 introduces a control element in the preparation of the gold nanoparticles that allows, in the particular experimental conditions here reported, to obtain very small (≈1 nm) AuNPs. These are the first experimental findings that identify a role of ligand "denticity" in the determination of the nuclearity of nanoparticles.

Monotopic and heteroditopic calix[4]arene receptors as hosts for pyridinium and viologen ion pairs: a solution and solid-state study.

The binding efficiency of a series of monotopic () and heteroditopic () calix[4]arene-based receptors has been evaluated in chloroform solution toward N-methylpyridinium ion pairs using NMR and UV/vis spectroscopic techniques. These experiments provided evidence that, due to a positive cooperative effect, the presence of a phenylurea H-bond donor group on the upper rim of the calix[4]arene macrocycle increases the recognition abilities of the heteroditopic receptors by up to two orders of magnitude with respect to the monotopic receptors. The heteroditopic receptors are also able to form 2:1 host-guest inclusion complexes with dimethylviologen salts both in low polarity solvents and in the solid state. These complexes are stabilized through the cooperation of weak (CH-pi and cation-pi) and strong (hydrogen bonding) intramolecular interactions between the binding domains of the calix[4]arene host and the two ions of the guest ion pair.

In Vitro Antiviral Activity of New Oxazoline Derivatives as Potent Poliovirus Inhibitors.

The final stages of polio eradication are proving more difficult than the early phases, and the development of effective drugs and treatments is considered a priority; thus, the research is ongoing. A screening of our in-house chemical library against poliovirus Sabin strains led to the identification of compounds 5 and 6 as hits active at submicromolar concentrations. Derivatives of these compounds were synthesized as a preliminary structure-activity-relationship study. Among them, 7 and 11 were highly active against poliovirus Sabin 1-3. Compound 11 was also very potent against a large panel of wild and vaccine-derived polioviruses. Time-of-addition experiments suggest that 5 and 7 could be active at an early stage of viral replication, whereas 11 was active at same concentration at all stages of viral replication. A ligand-based approach was applied to find the common structural features shared by the new compounds and already-known poliovirus inhibitors.

Design, Synthesis, and Biological Evaluation of New 1-(Aryl-1 H-pyrrolyl)(phenyl)methyl-1 H-imidazole Derivatives as Antiprotozoal Agents.

We have designed and synthesized a series of new imidazole-based compounds structurally related to an antiprotozoal agent with nanomolar activity which we identified recently. The new analogues possess micromolar activities against Trypanosoma brucei rhodesiense and Leishmania donovani and nanomolar potency against Plasmodium falciparum. Most of the analogues displayed IC50 within the low nanomolar range against Trypanosoma cruzi, with very high selectivity toward the parasite. Discussion of structure-activity relationships and in vitro biological data for the new compounds are provided against a number of different protozoa. The mechanism of action for the most potent derivatives (5i, 6a-c, and 8b) was assessed by a target-based assay using recombinant T. cruzi CYP51. Bioavailability and efficacy of selected hits were assessed in a T. cruzi mouse model, where 6a and 6b reduced parasitemia in animals >99% following intraperitoneal administration of 25 mg/kg/day dose for 4 consecutive days.

Biological evaluation and structure-activity relationships of imidazole-based compounds as antiprotozoal agents.

We discovered a series of azole antifungal compounds as effective antiprotozoal agents. They displayed promising inhibitory activities within the micromolar-submicromolar range against P. falciparum, L. donovani, and T. b. rhodesiense. Moreover, most of such compounds showed excellent nanomolar IC50 against T. cruzi, showing also very low cytotoxicity. Discussion of structure-activity relationships and biological data for these compounds are provided against the different parasites. To assess the mechanism of action against T. cruzi we proved that the most potent compounds (3b, 3j-l) inhibited the T. cruzi CYP51. Moreover, the most active derivative 3j dramatically reduced parasitemia in T. cruzi mouse model without acute toxicity.

Novel Symmetrical Benzazolyl Derivatives Endowed with Potent Anti-Heparanase Activity.

Heparanase is the only mammalian endo-ß-d-glucuronidase involved in a variety of major diseases. The up-regulation of heparanase expression increases tumor size, angiogenesis, and metastasis, representing a validated target in the anti-cancer field. To date, only a few small-molecule inhibitors have been described, but none have gotten through pre-clinical development. Previously, we explored 2-(4-(4-(bromo-methoxybenzamido)benzylamino)phenyl) benzazole derivatives as anti-heparanase agents, proposing this scaffold for development of broadly effective heparanase inhibitors. Herein, we report an extended investigation of new symmetrical 2-aminophenyl-benzazolyl-5-acetate derivatives, proving that symmetrical compounds are more effective than asymmetrical analogues, with the most-potent compound, 7g, being active at nanomolar concentration against heparanase. Molecular docking studies were performed on the best-acting compounds 5c and 7g to rationalize their interaction with the enzyme. Moreover, invasion assay confirmed the anti-metastatic potential of compounds 5c, 7a, and 7g, proving the inhibition of the expression of proangiogenic factors in tumor cells.

Novel Benzazole Derivatives Endowed with Potent Antiheparanase Activity.

Heparanase is the sole mammalian enzyme capable of cleaving glycosaminoglycan heparan sulfate side chains of heparan sulfate proteoglycans. Its altered activity is intimately associated with tumor growth, angiogenesis, and metastasis. Thus, its implication in cancer progression makes it an attractive target in anticancer therapy. Herein, we describe the design, synthesis, and biological evaluation of new benzazoles as heparanase inhibitors. Most of the designed derivatives were active at micromolar or submicromolar concentration, and the most promising compounds are fluorinated and/or amino acids derivatives 13a, 14d, and 15 that showed IC50 0.16-0.82 µM. Molecular docking studies were performed to rationalize their interaction with the enzyme catalytic site. Importantly, invasion assay confirmed the antimetastatic potential of compounds 14d and 15. Consistently with its ability to inhibit heparanase, compound 15 proved to decrease expression of genes encoding for proangiogenic factors such as MMP-9, VEGF, and FGFs in tumor cells.

Structure-Activity Relationships on Cinnamoyl Derivatives as Inhibitors of p300 Histone Acetyltransferase.

Human p300 is a polyhedric transcriptional coactivator that plays a crucial role in acetylating histones on specific lysine residues. A great deal of evidence shows that p300 is involved in several diseases, including leukemia, tumors, and viral infection. Its involvement in pleiotropic biological roles and connections to diseases provide the rationale to determine how its modulation could represent an amenable drug target. Several p300 inhibitors (i.e., histone acetyltransferase inhibitors, HATis) have been described so far, but they all suffer from low potency, lack of specificity, or low cell permeability, which thus highlights the need to find more effective inhibitors. Our cinnamoyl derivative, 2,6-bis(3-bromo-4-hydroxybenzylidene)cyclohexanone (RC56), was identified as an active and selective p300 inhibitor and was proven to be a good hit candidate to investigate the structure-activity relationship toward p300. Herein, we describe the design, synthesis, and biological evaluation of new HATis structurally related to our hit; moreover, we investigate the interactions between p300 and the best-emerged hits by means of induced-fit docking and molecular-dynamics simulations, which provided insight into the peculiar chemical features that influence their activity toward the targeted enzyme.

Diaryl Disulfides as Novel Stabilizers of Tumor Suppressor Pdcd4.

The translation inhibitor and tumor suppressor Pdcd4 was reported to be lost in various tumors and put forward as prognostic marker in tumorigenesis. Decreased Pdcd4 protein stability due to PI3K-mTOR-p70S6K1 dependent phosphorylation of Pdcd4 followed by ß-TrCP1-mediated ubiquitination, and proteasomal destruction of the protein was characterized as a major mechanism contributing to the loss of Pdcd4 expression in tumors. In an attempt to identify stabilizers of Pdcd4, we used a luciferase-based high-throughput compatible cellular assay to monitor phosphorylation-dependent proteasomal degradation of Pdcd4 in response to mitogen stimulation. Following a screen of approximately 2000 compounds, we identified 1,2-bis(4-chlorophenyl)disulfide as a novel Pdcd4 stabilizer. To determine an initial structure-activity relationship, we used 3 additional compounds, synthesized according to previous reports, and 2 commercially available compounds for further testing, in which either the linker between the aryls was modified (compounds 2-4) or the chlorine residues were replaced by groups with different electronic properties (compounds 5 and 6). We observed that those compounds with alterations in the sulfide linker completely lost the Pdcd4 stabilizing potential. In contrast, modifications in the chlorine residues showed only minor effects on the Pdcd4 stabilizing activity. A reporter with a mutated phospho-degron verified the specificity of the compounds for stabilizing the Pdcd4 reporter. Interestingly, the active diaryl disulfides inhibited proliferation and viability at concentrations where they stabilized Pdcd4, suggesting that Pdcd4 stabilization might contribute to the anti-proliferative properties. Finally, computational modelling indicated that the flexibility of the disulfide linker might be necessary to exert the biological functions of the compounds, as the inactive compound appeared to be energetically more restricted.

New insights into the interaction between pyrrolyl diketoacids and HIV-1 integrase active site and comparison with RNase H.

HIV-1 integrase (IN) inhibitors are one of the most recent innovations in the treatment of HIV infection. The selection of drug resistance viral strains is however a still open issue requiring constant efforts to identify new anti-HIV-1 drugs. Pyrrolyl diketo acid (DKA) derivatives inhibit HIV-1 replication by interacting with the Mg2+ cofactors within the HIV-1 IN active site or within the HIV-1 reverse-transcriptase associated ribonuclease H (RNase H) active site. While the interaction mode of pyrrolyl DKAs with the RNase H active site has been recently reported and substantiated by mutagenesis experiments, their interaction within the IN active site still lacks a detailed understanding. In this study, we investigated the binding mode of four pyrrolyl DKAs to the HIV-1 IN active site by molecular modeling coupled with site-directed mutagenesis studies showing that the DKA pyrrolyl scaffold primarily interacts with the IN amino residues P145, Q146 and Q148. Importantly, the tested DKAs demonstrated good effectiveness against HIV-1 Raltegravir resistant Y143A and N155H INs, thus showing an interaction pattern with relevant differences if compared with the first generation IN inhibitors. These data provide precious insights for the design of new HIV inhibitors active on clinically selected Raltegravir resistant variants. Furthermore, this study provides new structural information to modulate IN and RNase H inhibitory activities for development of dual-acting anti-HIV agents.

Structure-activity relationship of pyrrolyl diketo acid derivatives as dual inhibitors of HIV-1 integrase and reverse transcriptase ribonuclease H domain.

The development of HIV-1 dual inhibitors is a highly innovative approach aimed at reducing drug toxic side effects as well as therapeutic costs. HIV-1 integrase (IN) and reverse transcriptase-associated ribonuclease H (RNase H) are both selective targets for HIV-1 chemotherapy, and the identification of dual IN/RNase H inhibitors is an attractive strategy for new drug development. We newly synthesized pyrrolyl derivatives that exhibited good potency against IN and a moderate inhibition of the RNase H function of RT, confirming the possibility of developing dual HIV-1 IN/RNase H inhibitors and obtaining new information for the further development of more effective dual HIV-1 inhibitors.