Di-, tri- and tetra-5'-O-phosphorothioadenosyl substituted polyols as inhibitors of Fhit: Importance of the α-β bridging oxygen and β phosphorus replacement

Background  

The human FHIT gene is inactivated early in the development of many human cancers and loss of Fhit in mouse predisposes to cancer while reintroduction of FHIT suppresses tumor formation via induction of apoptosis. Fhit protein, a diadenosine polyphosphate hydrolase, does not require hydrolase activity to function in tumor suppression and may signal for apoptosis as an enzyme-substrate complex. Thus, high affinity nonhydrolyzable substrate analogs may either promote or antagonize Fhit function, depending on their features, in Fhit + cells. Previously synthesized analogs with phosphorothioadenosyl substitutions and "supercharged" branches do not bind better than natural substrates and thus have limited potential as cellular probes.     

New Tripodal, “Supercharged” Analogues of Adenosine Nucleotides: Inhibitors for the Fhit Ap3A Hydrolase

Methanetrisphosphonic acids provide a branch point for synthetic nucleotide analogues which can be exploited either to generate novel tripodal nucleotides or to incorporate additional negative charge into linear analogues relative to the parent nucleotide, as exemplified in the picture for ATP and diadenosine tetraphosphate (Ap₄A). These compounds show valuable discriminatory behavior as competitive inhibitors for the tumor suppressor protein Fhit and a second Ap_nA pyrophosphohydrolase. X=H, Cl, F.     

Selective Monitoring of the Enzymatic Activity of the Tumor Suppressor Fhit

Cancer is a leading cause of death worldwide. Functional inactivation of tumor suppressor proteins, mainly by mutations in the corresponding genes, is a key event in cancer development. The fragile histidine triade protein (Fhit) is a tumor suppressor that is frequently affected in different cancer types. Fhit possesses diadenosine triphosphate hydrolase activity, but although reduction of its enzymatic activity appears to be important for exerting its tumor suppressor function, the regulation of Fhit activity is poorly understood. Here, we introduce a novel fluorogenic probe that is suited to selectively analyze the enzymatic activity of Fhit in extracts derived from human cells. This novel method will allow in‐depth insight into the mechanisms involved in Fhit regulation in biologically relevant setups and, thus, into its role in the development of cancer.     

Tumor suppressor Fhit protein interacts with protoporphyrin IX in vitro and enhances the response of HeLa cells to photodynamic therapy

Fhit, the product of tumor suppressor fragile histidine triad (FHIT) gene, exhibits antitumor activity of still largely unknown cellular background. However, it is believed that Fhit-Ap(3)A or Fhit-AMP complex might act as a second class messenger in cellular signal transduction pathway involved in cell proliferation and apoptosis. We demonstrate here for the first time that the photosensitizer, protoporphyrin IX (which is a natural precursor of heme) binds to Fhit protein and its mutants in the active site in vitro. Furthermore, PpIX inhibits the enzymatic activity of Fhit. Simultaneously, PpIX shows lower binding capacity to mutant Fhit-H96N of highly reduced hydrolase activity. In cell-based assay PpIX induced HeLa cell death in Fhit and Fhit-H96N-dependent manner which was measured by means of MTT assay. Moreover, HeLa cells stably expressing Fhit or mutant Fhit-H96N were more susceptible to protoporphyrin IX-mediated photodynamic therapy (2J/cm(2)) than parental cells.     

Probing the Subunit-Subunit Interaction of the Tetramer of E. coli KDO8P Synthase by Electrospray Ionization Mass Spectrometry

Escherichia coli 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation reaction between D-arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P and inorganic phosphate (Pi). This enzyme exists as a tetramer in solution, which is important for catalysis. Two different states of the enzyme were obtained: i) PEP-bound and ii) PEP-unbound. The effect of the substrates and products on the overall structure of KDO8P synthase in both PEP-bound and unbound states was examined using electrospray ionization mass spectrometry. The analysis of our data showed that the complexes of the PEP-unbound enzyme with PEP (or Pi) favored the formation of monomers, while the complexes with A5P (or KDO8P) mainly favored dimers. The PEP-bound enzyme was found to exist in the monomer and dimer with a small amount of the tetramer, whereas the PEP-unbound form primarily exists in the monomer and dimer, and no tetramer was observed, suggesting that the bound PEP have a role in stabilization of the tetrameric structure. Taken together, the results imply that the addition of the substrates or products to the unbound enzyme may alter the subunit-subunit interactions and/or conformational change of the protein at the active site, and this study also demonstrates that the electrospray ionization mass spectrometric method may be a powerful tool in probing the subunit-subunit interactions and/or conformational change of multi-subunit protein upon binding to ligand.     

A Next-Generation Air-Stable Palladium(I) Dimer Enables Olefin Migration and Selective C−C Coupling in Air

We report a new air-stable Pd^I dimer, [Pd(μ-I)(PCy₂^tBu)]₂, which triggers E-selective olefin migration to enamides and styrene derivatives in the presence of multiple functional groups and with complete tolerance of air. The same dimer also triggers extremely rapid C−C coupling (alkylation and arylation) at room temperature in a modular and triply selective fashion of aromatic C−Br, C−OTf/OFs, and C−Cl bonds in poly(pseudo)halogenated arenes, displaying superior activity over previous Pd^I dimer generations for substrates that bear substituents ortho to C−OTf.     

Di‐μ2‐sulfito‐κ8O,O′:O′,O′′‐bis[(2,4,6‐tri‐2‐pyrid­yl‐1,3,5‐triazine‐κ3N2,N1,N6)cadmium(II)] octa­hydrate

The title compound, [Cd₂(SO₃)₂(C₁₈H₁₂N₆)₂]·8H₂O, is a dimer built up around a symmetry center, where the sulfite anion displays a so far unreported coordination mode in metal‐organic complexes; the anion binds as a μ₂‐sulfite‐κ⁴O,O′:O′,O′′ ligand to two symmetry‐related seven‐coordinate Cd^II cations, binding through its three O atoms by way of two chelate bites with an O atom in common, which acts as a bridge. The cation coordination is completed by a 2,4,6‐tri‐2‐pyridyl‐1,3,5‐triazine ligand acting in its usual tridentate mode.     

New Acyclic Dimers of Cholic Acid with Oxamide and Hydrazide Spacers

Summary. Three new acyclic dimers of cholic acid with oxamide and isomeric hydrazide (N,N′-diacylhydrazine) spacers were obtained. The oxamide spacers bind two identical steroidal subunits through position 3 (head-to-head dimer) or position 23 (tail-to-tail dimer). In the case of a third dimer the hydrazine moiety binds two molecules of cholic acid through position 24 (tail-to-tail dimer).     

Crystal Structure of β-Cyclodextrin-Felbinac Inclusion Complex

The crystal structure of the inclusion complex of β‐cyclodextrin (β‐CD) synthesized with felbinac (4‐biphenylacetic acid) was determined by single crystal X‐ray diffraction at 150 K. The complex contains two β‐CDs, two felbinac molecules, twenty‐two water molecules in the asymmetric unit, and could be formulated as (C₄₂H₇₀O₃₅)₂·(C₁₄H₁₂O₂)₂·22(H₂O). In the crystal lattice, the two β‐CD moieties form a head‐to‐head dimer jointed through hydrogen bonds, and the felbinacs that interact by face‐to‐face Π‐Π stacking are included in the β‐CD dimer cavity with their carboxyl groups protruding out from cavity opening. In crystals the dimer units of β‐CD are stacked in an intermediate type (IM) that consists of closely packed β‐CD dimer layers.     

Stability and Dynamics of Cyclic Diguanylic Acid in Solution

Cyclic diguanylic acid (CDG) is a ubiquitous messenger involved in bacterial signaling networks. Despite its central role in motility, biofilm formation, virulence, and flagellum development, fundamental properties such as its aggregation state are still poorly understood. Here the dynamics and stability of metal‐free and Mg²⁺‐bound CDG are characterized. Atomistic simulations establish that the CDG dimer is slightly favored (by ?5 kcal mol^?1) over its dissociated form (2 CDG), while the Mg²⁺ ion coordinated in the X‐ray structure readily dissociates from (CDG)₂ in solution and prefers water coordination. As a ligand in a protein, CDG binds both as a U‐shaped and a quasilinear monomer. The current results indicate that the energy difference between these two conformations is only a few kilocalories per mole, which explains the facile adaptation to different protein environments. This, together with the slight preference of (CDG)₂ over 2 CDG suggests that (CDG)₂ binding to a protein does probably not occur via sequential binding of two individual monomers.     

Structure-function relationships of a catalytically efficient β-<Emphasis Type="SmallCaps">D</Emphasis>-xylosidase

β-d-Xylosidase from Selenomonas ruminantium is revealed as the best catalyst known (k _cat, k _cat/K _m) for promoting hydrolysis of 1,4-β-d-xylooligosaccharides. ¹H nuclear magnetic resonance experiments indicate the family 43 glycoside hydrolase acts through an inversion mechanism on substrates 4-nitrophenyl-β-d-xylopyranoside (4NPX) and 1,4-β-d-xylobiose (X2). Progress curves of 4-nitrophenyl-β-d-xylobioside, xylotetraose and xylohexaose reactions indicate that one residue from the nonreducing end of substrate is cleaved per catalytic cycle without processivity. Values of k _cat and k _cat/K _m decrease for xylooligosaccharides longer than X2, illustrating the importance to catalysis of subsites −1 and +1 and the lack there of subsite +2. Homology models of the enzyme active site with docked substrates show that subsites bey ond−1 are blocked by protein and subsites bey ond +1 are not formed; they suggest that D14 and E186 serve catalysis as general base and general acid, respectively. Individual mutations, D14A and E186A, erode k _cat and k _cat/K _m by <10³ and to asimilar extent for substrates 4NPX and 4-nitrophenyl-α-l-arabinofuranoside (4NPA), indicating that the two substrates share the same active site. With 4NPX and 4NPA, pH governs k _cat/K _m with pK _a values of 5.0 and 7.0 assigned to D14 and E186, respectively. k _cat (4NPX) has a pK _a value of 7.0 and k _cat (4NPA) is pH independent above pH 4.0, suggesting that the catalytically inactive, “dianionic” enzyme form (D14-E187-) binds 4NPX but not 4NPA. The mention of firm names or trade products does not imply that they are end orsed or recommended by the US Department of Agriculture over other firms or similar products not mentioned.     

New Acyclic Dimers of Cholic Acid with Oxamide and Hydrazide Spacers

Three new acyclic dimers of cholic acid with oxamide and isomeric hydrazide (N,N′-diacylhydrazine) spacers were obtained. The oxamide spacers bind two identical steroidal subunits through position 3 (head-to-head dimer) or position 23 (tail-to-tail dimer). In the case of a third dimer the hydrazine moiety binds two molecules of cholic acid through position 24 (tail-to-tail dimer).     

Dimerization of C60: Symmetry Considerations

Orbital‐symmetry analysis (OCAMS) of the dimerization of C₆₀ via [2+2] cycloaddition indicates that the reactant monomers should approach one another along a pathway in which C_2h symmetry is conserved. Point‐by‐point computations (AM1/UHF) confirm this prediction: a low‐energy pathway leads to a single‐bonded dimer 2 with C_2h symmetry. Closure to the stable D_2h dimer 1 is effected by relatively facile rotation about the single bond. A similar symmetry analysis was performed on a second isomer 3 with D_2h symmetry, the moieties of which are linked by two two‐atom chains. It raises the possibility that 3 , the so‐called `window' isomer, may be interconvertible with 1 along a pathway that retains C_i (S₂) symmetry. Although the computational results indicate that C₆₀ is in thermal equilibrium with its stable dimer 1 at moderate temperatures, the latter is not observed in the gas phase for thermodynamic reasons. According to THERMO computations (AM1/RHF), the equilibrium is shifted strongly towards the monomer pair at temperatures where vaporization of the solid C₆₀ is observed (>400°).     

MnRe(CO)10: A review of the chemical and physical properties of a simple heterobimetallic non-bridged dimer

A review of the chemical and physical properties of MnRe(CO)₁₀ and its derivatives has been undertaken. This heterobimetallic complex is one of the simplest complexes known which contains a bond between two different metals and does not contain bridging groups. The review has revealed that high yield synthetic strategies are known for this complex and the synthetic strategies have bearing for the synthesis of other bimetallic complexes. Kinetic data suggest that information available on monometallic fragments can provide information on the reactivity trends expected for the dimer. However, the second metal is not a neutral spectator and provides a site forsecondary reactions eg for CO substitution. Data on the physical properties of the dimer are sparse and definitive statements ond _Mn-Re·v _Mn-Re, H_Mn-Re etc. cannot be made. This has significant implications for studies on related simple and complex dimer and cluster complexes.     

Diverse Modes of Guest Inclusion in a Cyclodextrin: X-ray Structural and Thermal Characterization of a 4:3 β-cyclodextrin—Cyclizine Complex

Abstract

1-Diphenylmethyl-4-methylpiperazine (cyclizine) is an antiemetic drug which forms an inclusion complex with β-cyclodextrin of formula (β-cyclodextrin)₄ · (cyclizine)₃ · 50H₂O. This species crystallizes in the monoclinic space group P2₁ with a = 15.246(1), b = 65.075(5), c = 15.609(1) Å, β = 102.62(1)° and Z = 2 formula units. Complex water content and the host:drug stoichiometric ratio were determined by thermogravimetry and UV spectrophotometry respectively. Differential scanning calorimetry showed that the crystals dehydrate in at least two stages and begin to decompose from approximately 250°C. The crystal structure was solved by a combination of Patterson search and direct methods. Isotropic refinement converged at R = 0.094 for 8806 reflections with I > 2σ(I). The unusual stoichiometry is accounted for as follows: the four β-cyclodextrin molecules comprising the asymmetric unit occur as two independent head-to-head dimers, each formed by O—H…O hydrogen bonding across the macro-cyclic secondary surfaces. One dimer contains two cyclizine guest molecules in head-to-tail orientation, thus accounting for two distinct modes of drug inclusion. In the second dimer, only one β-cyclodextrin molecule is significantly occupied by a cyclizine molecule (in a mode analogous to one of those in the first dimer), the other half of the dimer being largely devoid of guest. A possible mechanism for the formation of this unusual structure is proposed and the crystal packing arrangement is shown to be based on a novel disrupted tetrameric channel motif.     

Engineering human Fhit, a diadenosine triphosphate hydrolase, into an efficient dinucleoside polyphosphate synthase

The putative human tumor suppressor gene FHIT encodes Fhit, the fragile histidine triad protein. Fhit is thought to participate in a signal transduction pathway involving dinucleoside polyphosphates. Fhit catalyzes the Mg2+-dependent hydrolysis of P1-5'-O-adenosine-P3-5'-O-adenosine triphosphate (Ap3A) to AMP and MgADP. Mutation of His96 to glycine disables Fhit as a catalyst for the hydrolysis of phosphoanhydrides such as Ap3A. However, the mutated enzyme H96G-Fhit efficiently catalyzes the synthesis of phosphoanhydride bonds in reactions of nucleoside-5'-phosphimidazolides with nucleoside di- and triphosphates. H96G-Fhit can be employed in the synthesis of a wide range of dinucleoside tri- and tetraphosphates. We here describe the use of H96G-Fhit to catalyze the synthesis of Ap3A, Ap3C, Ap3G, Ap3T, Ap3U, Cp3U, Tp3U, dAp3U, Ap4A, Ap4U, and the fluorescent Ap4etheno-C.     

Protein Dimerization on a Phosphonated Calix[6]arene Disc

Complex formation between cationic cytochrome c and the water‐soluble, poly‐anionic p ‐phosphonatocalix[6]arene (pclx₆) was investigated. A crystal structure (at 1.8 Å resolution) revealed a remarkable dimeric disc of pclx₆ that acts like glue to mediate a symmetric (C ₂) protein dimer. The calixarene disc has a diameter of about 1.5 nm and masks about 360 Ų of protein surface. The key protein–calixarene contacts occur via two linchpin lysines, with additional contacts provided by a small hydrophobic patch. The protein–calixarene supramolecular assemblies were observed in solution by size‐exclusion chromatography with multi‐angle light scattering and NMR spectroscopy. Using isothermal titration calorimetry and NMR data, an apparent K _d in the low micromolar range was determined for the charge‐rich protein–calixarene complex. In contrast to p ‐sulfonatocalix[4]arene, the larger pclx₆ has a single, well‐defined binding site that mediates the assembly of cytochrome c in solution.     

Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer

SspB, a specificity factor for the ATP-dependent ClpXP protease, stimulates proteolysis of protein substrates bearing the ssrA degradation tag. The SspB protein is shown here to form a stable homodimer with two independent binding sites for ssrA-tagged proteins or peptides. SspB by itself binds to ClpX and stimulates the ATPase activity of this enzyme. In the presence of ATPgammaS, a ternary complex of SspB, GFP-ssrA, and the ClpX ATPase was sufficiently stable to isolate by gel-filtration or ion-exchange chromatography. This complex consists of one SspB dimer, two molecules of GFP-ssrA, and one ClpX hexamer. SspB dimers do not commit bound substrates to ClpXP degradation but increase the affinity and cooperativity of binding of ssrA-tagged substrates to ClpX, facilitating enhanced degradation at low substrate concentrations.     

Double Pancake Versus Long Chalcogen–Chalcogen Bonds in Six‐Membered C,N,S‐Heterocycles

The double “pancake” bonding in the dimers of the six‐membered heterocycles 1,3‐dithia‐2,4,6‐triazine ( 4 ) and 1,3‐dithia‐2,4‐diazine ( 16 ) were investigated by means of high‐level quantum chemical calculations (B3LYP and CCSD(T)). It was found that the S–S dimers, 20 a and 27 , are not the most stable isomers, but the dimers showing short S?N ( 21 a ) and S?C ( 25 , 28 ) bonds. An investigation of the 5‐phenyl‐1,3‐dithia‐2,4,6‐triazine ( 4 b ) yields that the syn dimer with two S?S bonds (2.57 Å) is the most stable one. In this dimer, the phenyl groups are placed on top of each other. The additional dispersion energy of the phenyl rings causes a stabilization of the syn‐S–S (C_2v‐like) isomer. As a result, two weak albeit relevant single S?S bonds (2.57 Å) are predicted. These findings contradict the recently published concept of double “pancake” bonding in the dimer 4 b ₂.     

Conformational Panorama and Chirality Controlled Structure–Energy Relationship in a Chiral Carboxylic Acid Dimer

Chirality recognition in dimers of tetrahydro-2-furoic acid (THFA) was studied in a conformer-specific manner using rotational spectroscopy and theoretical approaches. THFA shows a strong preference for the trans- over the cis-COOH configuration. Two drastically different scenarios are possible for the detectable (THFA)₂: a kinetically preferred dimer bound by feeble interactions between two trans THFAs or a thermodynamically favored dimer with a double hydrogen-bonded ring structure between two cis subunits. To identify the conformers responsible for the extremely dense rotational spectra observed, it was essential not only to locate several hundred homo/heterochiral (THFA)₂ minima in ab initio calculations but also to evaluate the energetic connectivities among the minima. The study further reveals an interesting chirality dependent structure–energy ordering relationship. A method for enantiomeric excess (ee) determination of THFA is presented using a recently proposed chiral self-tag approach.