Potent suppression of c-di-GMP synthesis via I-site allosteric inhibition of diguanylate cyclases with 2'-F-c-di-GMP.

Cyclic-di-GMP (c-di-GMP) is a central regulator of bacterial behavior. Various studies have implicated c-di-GMP in biofilm formation and virulence factor production in multitudes of bacteria. Hence it is expected that the disruption of c-di-GMP signaling could provide an effective means to disrupt biofilm and/or virulence factor formation in several bacteria of clinical relevance. C-di-GMP achieves the regulation of bacterial phenotype via binding to several effector molecules including transcription factors, enzymes and riboswitches. Crystal structure analyses of c-di-GMP effector molecules, in complex with the ligand, reveal that various classes of c-di-GMP receptors recognize this dinucleotide using different sets of recognition elements. Therefore, it is plausible that different analogues of c-di-GMP could be used to selectively modulate a specific class of c-di-GMP binding receptors, and hence modulate the bacterial phenotype. Thus far only a detailed study of the differential binding of c-di-GMP analogues to riboswitches, but not proteins, has been reported. In this report, we prepared various 2'-modified analogues of c-di-GMP and studied both polymorphisms of these analogues using DOSY NMR and the binding to several effector proteins, such as PilZ-containing proteins, diguanylate cyclases (DGC) containing I-sites, and phoshphodiesterases (PDE). 2'-Modification of c-di-GMP did not adversely affect the propensity to form higher aggregates, such as octameric forms, in the presence of potassium salts. Interestingly, we find that the selective binding to different classes of c-di-GMP binding proteins could be achieved with the 2'-modified analogues and that 2'-F analogue of c-di-GMP binds to the I-site of DGCs better (four times) than the native dinucleotide, c-di-GMP, whereas c-di-GMP binds to PDEs better (10 times) than 2'-F-c-di-GMP. 2'-F-c-di-GMP potently inhibits c-di-GMP synthesis by DGCs and hence raises the potential that cell permeable analogues of 2'-F-c-di-GMP could be used to disrupt c-di-GMP signaling in bacteria.

Surprising acid/base and ion-sequestration chemistry of Sn9(4-): HSn9(3-), Ni@HSn9(3-), and the Sn9(3-) ion revisited.

K(4)Sn(9) dissolves in ethylenediamine (en) to give equilibrium mixtures of the diamagnetic HSn(9)(3-) ion along with K(x)Sn(9)((4-x)-) ion pairs, where x = 0, 1, 2, 3. The HSn(9)(3-) cluster is formed from the deprotonation of the en solvent and is the conjugate acid of Sn(9)(4-). DFT studies show that the structure is quite similar to the known isoelectronic RSn(9)(3-) ions (e.g., R = i-Pr). The hydrogen atom of HSn(9)(3-) (δ = 6.18 ppm) rapidly migrates among all nine Sn atoms in an intramolecular fashion; the Sn(9) core is also highly dynamic on the NMR time scale. The HSn(9)(3-) cluster reacts with Ni(cod)(2) to give the Ni@HSn(9)(3-) ion containing a hydridic hydrogen (δ = -28.3 ppm) that also scrambles across the Sn(9) cluster. The Sn(9)(4-) ion competes effectively with 2,2,2-crypt for binding K(+) in en solutions, and the pK(a) of HSn(9)(3-) is similar to that of en (i.e., Sn(9)(4-) is a very strong Brønsted base with a pK(b) comparable to that of the NH(2)CH(2)CH(2)NH(-) anion). Competition studies show that the HSn(9)(3-) ⇄ Sn(9)(4-) + H(+) equilibrium is fully reversible. The HSn(9)(3-) anion is present in significant concentrations in en solutions containing 2,2,2-crypt, yet it has gone undetected for over 30 years.

Conservative change to the phosphate moiety of cyclic diguanylic monophosphate remarkably affects its polymorphism and ability to bind DGC, PDE, and PilZ proteins.

The cyclic dinucleotide c-di-GMP is a master regulator of bacterial virulence and biofilm formation. The activations of c-di-GMP metabolism proteins, diguanylate cyclases (DGCs) and phosophodiesterases (PDEs), usually lead to diametrically opposite phenotypes in bacteria. Analogues of c-di-GMP, which can selectively modulate the activities of c-di-GMP processing proteins, will be useful chemical tools for studying and altering bacterial behavior. Herein we report that a conservative modification of one of the phosphate groups in c-di-GMP with a bridging sulfur in the phosphodiester linkage affords an analogue called endo-S-c-di-GMP. Computational, NMR (including DOSY), and CD experiments all reveal that, unlike c-di-GMP, endo-S-c-di-GMP does not readily form higher aggregates. The lower propensity of endo-S-c-di-GMP to form aggregates (as compared to that of c-di-GMP) is probably due to a higher activation barrier to convert from the "open" conformer (where the two guanines are on opposite faces) to the "closed" conformer (where the two guanines are on the same face). Consequently, endo-S-c-di-GMP has selectivity for proteins that bind monomeric but not dimeric c-di-GMP, which form from the "closed" conformer. For example, endo-S-c-di-GMP can inhibit the hydrolysis of c-di-GMP by RocR (a PDE enzyme that binds monomeric c-di-GMP) but did not bind to Alg44 (a PilZ protein) or regulate WspR (a DGC enzyme that has been shown to bind to dimeric c-di-GMP). This work demonstrates that selective binding to different classes of c-di-GMP binding proteins could be achieved by altering analogue conformer populations (conformational steering). We provide important design principles for the preparation of selective PDE inhibitors and reveal the role played by the c-di-GMP backbone in c-di-GMP polymorphism and binding to processing proteins.

Trapping a labile adduct formed between an ortho-quinone methide and 2'-deoxycytidine.

Selective oxidation by bis[(trifluoroacetoxy)iodo]benzene (BTI) provides an effective trap for quenching adducts formed reversibly between dC and an ortho-quinone methide (QM) under physiological conditions. A model adduct generated by 4-methyl-o-QM and 2'-deoxycytidine is rapidly converted by intramolecular cyclization and loss of aromaticity to a characteristic product for quantifying QM alkylation. However, BTI induces a surprising rearrangement driven by overoxidation of a derivative lacking an alkyl substituent at the 4-position of the QM.

Prefluorescent nitroxide probe for the highly sensitive determination of peroxyl and other radical oxidants.

Fluorescamine derivatized 3-amino-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (I) is shown to undergo an irreversible reaction with peroxyl radicals and other radical oxidants to generate a more highly fluorescent diamagnetic product (II) and thus can be used as a highly sensitive and versatile probe to determine oxidant production optically, either by monitoring the changes in fluorescence intensity, by HPLC analysis with fluorescence detection, or by a combination of both approaches. By changing the [O2]/[I] ratio, we show that peroxyl radicals can be detected and quantified preferentially in the presence of other radical oxidants. Detection of photochemically produced peroxyl radicals is achieved by employing 3-amino-2,2,5,5,-tetramethyl-1-pyrrolidinyloxy (3-ap) alone, followed by derivatization with fluorescamine. With employment of HPLC analysis, the detection limit of II at a S/N of 2 is approximately 3 nM for a 125 microL injection. Preliminary applications include the detection of peroxyl radicals generated thermally in soybean phosphatidylcholine liposomes and produced photochemically in tap water.

Substituent-dependent exchange mechanisms in highly fluxional RSn9(3-) anions.

119Sn NMR studies show that the RSn9(3-) ions (R=i-Pr, Sn(C6H11)3) are highly fluxional in solution, where the exchange mechanisms involve rapid migration of the R group in the latter but not in the former.

Solution dynamics and gas-phase chemistry of Pd2@Sn18 4-.

Sn9(4-) reacts with Pd(PPh3)4 in ethylenediamine/toluene solvent mixtures in the presence of 2,2,2-cryptand to give the Pd2@Sn18(4-) cluster as the K(2,2,2,-crypt)+ salt. The cluster is isostructural with Pd2@Ge18(4-) and has a nuclearity different from that of the Pt and Ni analogues, Ni2@Sn17(4-) and Pt2@Sn17(4-). The Pd2@Sn18(4-) ion has a deltahedral capsulelike structure with 40 cluster bonding electrons and is the largest free-standing polystannide characterized to date. Like Pt2@Sn17(4-), the Pd2@Sn18(4-) complex is highly dynamic in solution, showing a single (119)Sn NMR resonance indicative of an intramolecular liquidlike dynamic exchange. LDI-MS studies of the crystalline sample show extensive fragmentation and the formation of five gas-phase cluster series: Sn(x)- (1 < x < 12), PdSn(x-1) - (4 < x < 18), Pd 2Sn(x-2) - (6 < x < 21), Pd3Sn(x-3) - (8 < x < 21), and Pd 4Sn(x-4) - (13 < x < 21). The most abundant ion in the gas phase is the PdSn(10) - cluster, which presumably has an Sn(10) bicapped-square-antiprismatic structure with an endohedral Pd (e.g., Ni@Pb(10)(2-)).

Refolding foldamers: triazene-arylene oligomers that change shape with chemical stimuli.

We describe the preparation of five triazene-arylene oligomers (3, 4, 7, 8, and 11) and investigations of their folding properties in aqueous solution. These oligomers contain four 2-fold rotors and populate a conformational ensemble comprising at least 10 states. Extensive 1D and 2D NMR studies as well as X-ray crystallography establish that the presence of three members of the cucurbit[n]uril family (CB[n]), CB[10], CB[7], and CB[8], results in the selective population of the (a,a,a,a)-, (a,s,s,a)-, and (a,a,a,s)-conformers. As a result of the high affinity and highly selective binding properties of the CB[n] family, it is possible to fold a single foldamer strand (3) into the CB[8].(a,a,a,s)-3 conformer by the addition of CB[8], then unfold and refold it into the CB[7].(a,s,s,a)-3.CB[7] conformer by addition of CB[7] and 3,5-dimethylaminoadamantane (17), then unfold and refold it again into the CB[10].(a,a,a,a)-3 conformer by addition of CB[10].CB[5] and aminoadamantane (18). The transformation of CB[8].(a,a,a,s)-3 into CB[7].(a,s,s,a)-3.CB[7] proceeds through the intermediacy of CB [8].(a,a,s,a)-3.CB[7], which enhances the rate of dissociation of strand 3 from CB[8].

Cluster growth and fragmentation in the highly fluxional platinum derivatives of Sn9 4-: synthesis, characterization, and solution dynamics of Pt2@Sn17 4- and Pt@Sn9H 3-.

Sn94- reacts with Pt(PPh3)4 in ethylenediamine/toluene solvent mixtures in the presence of 2,2,2-cryptand to give four different complexes: "Rudolph's complex" of proposed formula [Sn9Pt(PPh3)x]4- (2), the previously reported [Pt@Sn9Pt(PPh3)]2- ion (3), and the title complexes Pt2@Sn174- (4) and Pt@Sn9H3- (5). The use of Pt(norbornene)3 instead of Pt(PPh3)4 gives complex 4 exclusively. The structure of 4 contains two Pt atoms centered in a capsule-shaped Sn17 cage. The complex is highly dynamic in solution showing single, mutually coupled 119Sn and 195Pt NMR resonances indicative of an intramolecular liquidlike dynamic exchange process. Complex 5 has been characterized by selectively decoupled 1H, 119Sn, and 195Pt NMR experiments and shows similar liquidlike fluxionality. In addition, the H atom scrambles across the cage showing small couplings to both Sn and Pt atoms. Neither 3 nor 4 obeys Wades rules; they adopt structures more akin to the subunits in alloys such as PtSn4. The structural and chemical relevance to supported PtSn4 heterogeneous catalysts is discussed.

Cation exchange in lipophilic G-quadruplexes: not all ion binding sites are equal.

Lipophilic guanosine derivatives that form G-quadruplexes are promising building blocks for ionophores and ion channels. Herein, cation exchange between solvated cations (K+ and NH4+) and bound cations in the G-quadruplex [G1]16.4Na+.4DNP- was studied by electrospray ionization mass spectrometry and solution 1H, 15N NMR spectroscopy. The ESI-MS and 1H NMR data provided evidence for the formation of mixed-cationic Na+, K+ G-quadruplexes. The use of 15NH4+ cations in NMR titrations, along with 15N-filtered 1H NMR and selective NOE experiments, identified two mixed-cationic intermediates in the cation exchange pathway from [G1]16.4Na+.4DNP- to [G1]16.4NH4+.4DNP-. The central Na+, bound between the two symmetry-related G8-Na+ octamers, exchanges with either K+ or NH4+ before the two outer Na+ ions situated within the C4 symmetric G8 octamers. A structural rationale, based on differences in the cations' octahedral coordination geometries, is proposed to explain the differences in site exchange for these lipophilic G-quadruplexes. Large cations such as Cs+ can be exchanged into the central cation binding site that holds the two symmetry-related C4 symmetric G8 octamer units together. The potential relevance of these findings to both supramolecular chemistry and DNA G-quadruplex structure are discussed.

Water-mediated association provides an ion pair receptor.

In this paper, we report on the formation and properties of a water-stabilized dimer comprising calix[4]arene-guanosine conjugate cG 2. The 1,3-alternate calixarene cG 2 was poorly soluble in dry CDCl(3) and gave an ill-resolved NMR spectrum, consistent with its nonspecific aggregation. The compound was much more soluble in water-saturated CDCl(3). Two sets of well-resolved (1)H NMR signals for the guanosine residues in cG 2, present in a 1:1 ratio, indicated that the compound's D(2) symmetry had been broken and provided the first hint that cG 2 dimerizes in water-saturated CDCl(3). The resulting dimer, (cG 2)(2).(H(2)O)(n)(), has a unique property: it extracts alkali halide salts from water into organic solution. This dimer is a rare example of a self-assembled ion pair receptor. The identity of the (cG 2)(2).NaCl.(H(2)O)(n)() dimer was confirmed by comparing its self-diffusion coefficient in CDCl(3), determined by pulsed-field gradient NMR, with that of control compound cA 3, an adenosine analogue. The dimer's stoichiometry was also confirmed by quantitative measurement of the cation and anion using ion chromatrography. Two-dimensional NMR and ion-induced NMR shifts indicated that the cation binding site is formed by an intermolecular G-quartet and the anion binding site is provided by the 5'-amide NH groups. Once bound, the salt increases the dimer's thermal stability. Both (1)H NMR and ion chromatography measurements indicated that the cG 2 dimer has a modest selectivity for extracting K(+) over Na(+) and Br(-) over Cl(-). The anion's identity also influences the association process: NaCl gives a soluble, discrete dimer whereas addition of NaBPh(4) to (cG 2)(2).(H(2)O)(n)() leads to extensive aggregation and precipitation. This study suggests a new direction for ion pair receptors, namely, the use of molecular self-assembly. The study also highlights water's ability to stabilize a functional noncovalent assembly.

Chloride transport across lipid bilayers and transmembrane potential induction by an oligophenoxyacetamide.

This contribution describes the discovery and properties of a synthetic, low-molecular weight compound that transports Cl- across bilayer membranes. Such compounds have potential as therapeutics for cystic fibrosis and cancer. The H+/Cl- co-transport activities of acyclic tetrabutylamides 1-6 were compared by using a pH-stat assay with synthetic EYPC liposomes. The ion transport activity of the most active compound, trimer 3, was an order of magnitude greater than that of calix[4]arene tetrabutylamide C1 a macrocycle known to function as a synthetic ion channel. Trimer 3 has an unprecedented function for a synthetic compound, as it induces a stable potential in liposomes experiencing a transmembrane Cl-/SO42- gradient. Data from both pH-stat and 35Cl NMR experiments indicate that 3 co-transports H+/Cl-. Although 3 transports both Cl- and H+ the overall process is not electrically silent. Thus, trimer 3 induces a stable potential in LUVs due to a transmembrane anionic gradient. The ability of trimer 3 to transport Cl-, to maintain a transmembrane potential, along with its high activity at uM concentrations, its low molecular weight, and its simple preparation, make this compound a valuable lead in drug development for diseases caused by Cl- transport malfunction.

Cyclometalated products of [(COE)(2)RhCl](2) and 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)Bu, (i)Pr) Are Dimeric. Synthesis, molecular structures, and solution dynamics of [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2).

Two tridentate thioether pincer ligands, 1,3-(RSCH(2))(2)C(6)H(4) (R = (t)()Bu, 1a; R = (i)()Pr, 1b) underwent cyclometalation using [(COE)(2)RhCl](2) in air/moisture-free benzene at room temperature. The resultant complexes, [mu-ClRh(H)(RSCH(2))(2)C(6)H(3)-2,6](2) (R = (t)Bu, 2a; R = (i)Pr, 2b) are dimeric both in the solid state and in solution. A battery of variable-temperature one- and two-dimensional (1)H NMR experiments showed conclusively that both complexes undergo dynamic exchange in solution. Exchange between two dimeric diastereomers of 2a in solution occurred via rotation about the Rh-C(ipso) bond. The dynamic exchange of 2b was significantly more complex as an additional exchange mechanism, sulfur inversion, occurred, which resulted in the exchange between several diastereomers in solution.