Three-Component Self-Assembly of a Series of Triply Interlocked Pd12 Coordination Prisms and Their Non-Interlocked Pd6 Analogues

Template-assisted formation of multicomponent Pd6 coordination prisms and formation of their self-templated triply interlocked Pd12 analogues in the absence of an external template have been established in a single step through Pd?N/Pd?O coordination. Treatment of cis-[Pd(en)(NO3)2] with K3tma and linear pillar 4,4'-bpy (en=ethylenediamine, H3tma=benzene-1,3,5-tricarboxylic acid, 4,4'-bpy=4,4'-bipyridine) gave intercalated coordination cage [{Pd(en)}6(bpy)3(tma)2]2[NO3]12 (1) exclusively, whereas the same reaction in the presence of H3tma as an aromatic guest gave a H3tma-encapsulating non-interlocked discrete Pd6 molecular prism [{Pd(en)}6(bpy)3(tma)2(H3tma)2][NO3]6 (2). Though the same reaction using cis-[Pd(NO3)2(pn)] (pn=propane-1,2-diamine) instead of cis-[Pd(en)(NO3)2] gave triply interlocked coordination cage [{Pd(pn)}6(bpy)3(tma)2]2[NO3]12 (3) along with non-interlocked Pd6 analogue [{Pd(pn)}6(bpy)3(tma)2](NO3)6 (3'), and the presence of H3tma as a guest gave H3tma-encapsulating molecular prism [{Pd(pn)}6(bpy)3(tma)2(H3tma)2][NO3]6 (4) exclusively. In solution, the amount of 3' decreases as the temperature is decreased, and in the solid state 3 is the sole product. Notably, an analogous reaction using the relatively short pillar pz (pz=pyrazine) instead of 4,4'-bpy gave triply interlocked coordination cage [{Pd(pn)}6(pz)3(tma)2]2[NO3]12 (5) as the single product. Interestingly, the same reaction using slightly more bulky cis-[Pd(NO3)2(tmen)] (tmen=N,N,N',N'-tetramethylethylene diamine) instead of cis-[Pd(NO3)2(pn)] gave non-interlocked [{Pd(tmen)}6(pz)3(tma)2][NO3]6 (6) exclusively. Complexes 1, 3, and 5 represent the first examples of template-free triply interlocked molecular prisms obtained through multicomponent self-assembly. Formation of the complexes was supported by IR and multinuclear NMR (1H and 13C) spectroscopy. Formation of guest-encapsulating complexes (2 and 4) was confirmed by 2D DOSY and ROESY NMR spectroscopic analyses, whereas for complexes 1, 3, 5, and 6 single-crystal X-ray diffraction techniques unambiguously confirmed their formation. The gross geometries of H3tma-encapsulating complexes 2 and 4 were obtained by universal force field (UFF) simulations.

Coordination-Driven Self-Assembly of 2D-Metallamacrocycles Using a New Carbazole-Based Dipyridyl Donor: Synthesis, Characterization, and C-60 Binding Study

A new carbazole-based 90 degrees dipyridyl donor 3,6-di(4-pyridylethynyl)carbazole (L) containing carbazole-ethynyl functionality is synthesized in reasonable yield using the Sonagashira coupling reaction. Multinuclear NMR, electrospray ionization-mass spectrometry (ESI-MS), including single crystal X-ray diffraction analysis characterized this 90 degrees building unit. The stoichiometry combination of L with several Pd(II)/Pt(II)-based 90 degrees acceptors (1a-1d) yielded 2 + 2] self-assembled metallacycles (2a-2d) under mild conditions in quantitative yields 1a = cis-(dppf)Pd(OTf)(2); 1b = cis-(dppf)Pt(OTf)(2); 1c = cis-(tmen)Pd(NO3)(2); 1d = 3,6-bis{trans-Pt(C C) (PEt3)(2)(NO3))carbazole]. All these macrocycles were characterized by various spectroscopic techniques, and the molecular structure of 2a was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of ethynyl functionality to the carbazole backbone causes the resulted macrocycles (2a-2d) to be pi-electron rich and thereby exhibit strong emission characteristics. The macrocycle 2a has a large internal concave aromatic surface. The fluorescence quenching study suggests that 2a forms a similar to 1:1 complex with C-60 with a high association constant of K-sv = 1.0 X 10(5) M-1.

Regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C through the transcriptional repression of upstream activating sequence inositol containing genes

The regulation of phospholipid biosynthesis in Saccharomyces cerevisiae through cis-acting upstream activating sequence inositol (UAS(ino)) and trans-acting elements, such as the INO2-INO4 complex and OPI1 by inositol supplementation in growth is thoroughly studied. In this study, we provide evidence for the regulation of lipid biosynthesis by phosphatidylinositol-specific phospholipase C (PLC) through UAS(ino) and the trans-acting elements. Gene expression analysis and radiolabelling experiments demonstrated that the overexpression of rice PLC in yeast cells altered phospholipid biosynthesis at the levels of transcriptional and enzyme activity. This is the first report implicating PLC in the direct regulation of lipid biosynthesis. (C) 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Sm(III)nitrate-catalyzed one-pot synthesis of furano3,2c]-1,2,3,4-tetrahydroquinolines and DNA photocleavage studies

The synthesis and DNA photocleavage studies of furano3,2-c]-1,2,3,4-tetrahydroquinolines have been reported. Sm(III)nitrate was found to be an efficient for the Diels-Alder reaction of aryl amines with 2,3-dihydrofuran to offer the corresponding furano3,2-c]-1,2,3,4-tetrahydroquinolines derivatives as a mixture of cis/trans stereoisomers in moderate yields. The aqueous solubility of acid catalyst can be recycled without significant loss of activity. The DNA photocleavage studies shows that, the cis/trans stereoisomers are good DNA cleavage mimic in terms of molecular structure. (C) 2012 Elsevier B.V. All rights reserved.

A Series of Trifacial Pd6 Molecular Barrels with Porphyrin Walls

Three new nanoscopic trigonal prisms, (tmen)6Pd6(H2L)3](NO3)12 (1), (Meen)6Pd6(H2L)3](NO3)12 (2), and (2,2'-bipy)6Pd6(H2L)3](NO3)12 (3), have been synthesized in excellent yields through single-step metalligand-coordination-driven self-assembly using 5,10,15,20-tetrakis(3-pyridyl)porphyrin (H2L) as a donor and cis-blocked PdII 90 degrees acceptors. These complexes were fully characterized by spectroscopic studies and single-crystal X-ray diffraction. All of these barrels quantitatively bind ZnII ions in the N4 pockets of the porphyrin walls at room temperature. Their corresponding zinc-embedded complexes, (tmen)6Pd6(ZnL)3](NO3)12 (1?a), (Meen)6Pd6(ZnL)3](NO3)12 (2?a), and (2,2'-bipy)6Pd6(ZnL)3](NO3)12 (3?a), were synthesized under ambient conditions by the post-synthetic binding of ZnII ions into the H2N4 pockets of the porphyrin walls of these complexes. These zinc-embedded complexes were characterized by electronic absorption, fluorescence emission, 1H NMR spectroscopy, as well as elemental analysis. Complexes 13 exhibited considerable microporosity in their solid state. Complex 1 was an efficient adsorbent for nitrogen gas and EtOH, MeOH, and water vapors.

An Antitubulin Agent BCFMT Inhibits Proliferation of Cancer Cells and Induces Cell Death by Inhibiting Microtubule Dynamics

Using cell based screening assay, we identified a novel anti-tubulin agent (Z)-5-((5-(4-bromo-3-chlorophenyl)furan-2-yl)methylene)-2-thioxothiazoli din-4-one (BCFMT) that inhibited proliferation of human cervical carcinoma (HeLa) (IC50, 7.2 +/- 1.8 mu M), human breast adenocarcinoma (MCF-7) (IC50, 10.0 +/- 0.5 mu M), highly metastatic breast adenocarcinoma (MDA-MB-231) (IC50, 6.0 +/- 1 mu M), cisplatin-resistant human ovarian carcinoma (A2780-cis) (IC50, 5.8 +/- 0.3 mu M) and multi-drug resistant mouse mammary tumor (EMT6/AR1) (IC50, 6.5 +/- 1 mu M) cells. Using several complimentary strategies, BCFMT was found to inhibit cancer cell proliferation at G2/M phase of the cell cycle apparently by targeting microtubules. In addition, BCFMT strongly suppressed the dynamics of individual microtubules in live MCF-7 cells. At its half maximal proliferation inhibitory concentration (10 mu M), BCFMT reduced the rates of growing and shortening phases of microtubules in MCF-7 cells by 37 and 40%, respectively. Further, it increased the time microtubules spent in the pause (neither growing nor shortening detectably) state by 135% and reduced the dynamicity (dimer exchange per unit time) of microtubules by 70%. In vitro, BCFMT bound to tubulin with a dissociation constant of 8.3 +/- 1.8 mu M, inhibited tubulin assembly and suppressed GTPase activity of microtubules. BCFMT competitively inhibited the binding of BODIPY FL-vinblastine to tubulin with an inhibitory concentration (K-i) of 5.2 +/- 1.5 mu M suggesting that it binds to tubulin at the vinblastine site. In cultured cells, BCFMT-treatment depolymerized interphase microtubules, perturbed the spindle organization and accumulated checkpoint proteins (BubR1 and Mad2) at the kinetochores. BCFMT-treated MCF-7 cells showed enhanced nuclear accumulation of p53 and its downstream p21, which consequently activated apoptosis in these cells. The results suggested that BCFMT inhibits proliferation of several types of cancer cells including drug resistance cells by suppressing microtubule dynamics and indicated that the compound may have chemotherapeutic potential.

Novel ATPase activity of the polyprotein intermediate, Viral Protein genome-linked-Nuclear Inclusion-a protease, of Pepper vein banding potyvirus

Potyviruses temporally regulate their protein function by polyprotein processing. Previous studies have shown that VPg (Viral Protein genome-linked) of Pepper vein banding virus interacts with the NIa-Pro (Nuclear Inclusion-a protease) domain, and modulates the kinetics of the protease. In the present study, we report for the first time that VPg harbors the Walker motifs A and B, and the presence of NIa-Pro, especially in cis (cleavage site (E191A) VPg-Pro mutant), is essential for manifestation of the ATPase activity. Mutation of Lys47 (Walker motif A) and Asp88:Glu89 (Walker motif B) to alanine in E191A VPg-Pro lead to reduced ATPase activity, confirming that this activity was inherent to VPg. We propose that potyviral VPg, established as an intrinsically disordered domain, undergoes plausible structural alterations upon interaction with globular NIa-Pro which induces the ATPase activity. (C) 2012 Elsevier Inc. All rights reserved.

Cyclodextrin and its complexation for resolution of isomers using diffusion ordered spectroscopy

Diffusion ordered spectroscopy (DOSY) generally fails to separate the peaks pertaining to isomeric species possessing identical molecular weights and similar hydrodynamic radii. The present study demonstrates the resolution of isomers using alpha/beta-cyclodextrin as a co-solute by Matrix Assisted Diffusion Ordered Spectroscopy. The resolution of isomers has been achieved by measuring the significant differences in the diffusion rates between the positional isomers of aminobenzoic acids, benzenedicarboxylic acids and between the cis, trans isomers, fumaric acid and maleic acid. (C) 2012 Elsevier B.V. All rights reserved.

Dual Role of Acetate as a Nucleophile and as an Internal Base in Cycloplatination Reaction of sym-N,N `,N `'-Triarylguanidines

Reaction of cis-Cl2Pt(S(O)Me-2)(2)] with 1 equiv of sym-N,N',N `'-triarylguanidines, ArN=C(NHAr)(2) (sym = symmetrical; Ar = 2-MeC6H4 (LH22-tolyl), 2-(MeO)C6H4 (LH22-anisyl), 4-MeC6H4 (LH24-tolyl), 2,5-Me2C6H3 (LH22,5-xylyl), and 2,6-Me2C6H3 (LH22,6-xylyl)) in toluene under reflux condition for 3 h afforded cis- or trans-Cl2Pt(S(O)Me-2)(ArN=C(NHAr)(2))] (Ar = 2-MeC6H4 (1), 2-(MeO)C6H4 (2), 4-MeC6H4 (3), 2,5-h Me2C6H3 (4), and 2,6-Me2C6H3 (5), respectively) in 83-96% yield. Reaction of cis-Cl2Pt(S(O)Me-2)(2)] with 1 equiv of LH22-tolyl and LH24-tolyl in the presence of 1 equiv of NaOAc in methanol under reflux condition for 3 h afforded acetate-substituted products, cis-(AcO)ClPt(S(O)Me-2)(ArN=C(NHAr)(2))] (Ar = 2-MeC6H4 (6) and 4-MeC6H4 (7)) in 83% and 84% yields, respectively. Reaction of cis-Cl2Pt(S(O)Me-2)(2)] with 1 equiv of LH22-anisyl and LH22-tolyl in the presence of 1 equiv of NaOAc in methanol under reflux condition for 3 and 12 h afforded six-membered C,N] platinacycles, Pt{kappa(2)(C,N)-C6H3R-3(NHC(NHAr)(=NAr))-2}Cl(S(O)Me-2)] (Ar = 2-RC6H4; R = OMe (8) and Me (9)), in 92% and 79% yields, respectively. The new complexes have been characterized by analytical and spectroscopic techniques, and further the molecular structures of 1, 2, 4, 5, 6, and 8 have been determined by single-crystal X-ray diffraction. The platinum atom in 1, 4, and 5 exhibited the trans configuration, while that in 2, 6, and 8 exhibited the cis configuration. Complex 6 is shown to be the precursor for 9, and the former is suggested to transform to the latter possibly via an intramolecular C-H activation followed by elimination of AcOH. The solution behavior of new complexes has been studied by multinuclear NMR (H-1, Pt-195, and C-13) spectroscopy. The new complexes exist exclusively as a single isomer (trans (1 and 5) and cis (6 and 7)), a mixture of cis and trans isomers with the former isomer being predominant in the case of 2 and the latter isomer being predominant in the case of 3. Complex 5 in the trans form revealed the presence of one isomer at 0.007 mM concentration and two isomers in about 1.00:0.12 ratio at 0.154 mM concentration as revealed by H-1 NMR spectroscopy, and this has been ascribed to the restricted Pt-S bond rotation at higher concentration. Platinacycle 8 exists as one isomer, while 9 exists as a mixture of seven isomers in solution. The influence of steric factor, pi-acceptor property of the guanidine, subtle solid-state packing forces upon the configuration of the platinum atom, and the number of isomers in solution have been outlined. Factors that accelerate or slow down the cycloplatination reaction, the role of NaOAc, and a plausible mechanism of this reaction have been discussed.

Multicomponent self-sorting of a Pd-7 molecular boat and its use in catalytic Knoevenagel condensation

Unique three-component self-assembly of a cis-blocked 90 degrees Pd(II) acceptor with amixture of tri- and tetra-imidazole donors led to the self-sorting of a Pd-7 molecular boat with an internal nanocavity, which catalyses the Knoevenagel condensation of a series of aromatic aldehydes with 1,3-dimethylbarbituric acid and Meldrum's acid in aqueous media.

Influence of steric effect on the structural aspects of N,N `,N `'-triarylguanidine derived six-membered C,N] palladacycles

Guanidine derived six-membered C,N] palladacycles of the types (C,N)Pd(mu-OC(O)R)](2) (1a-d), (C,N)Pd(mu-Br)](2) (2a,b), cis-(C,N)PdBr(L)] (3a-d, 4, and 5), and ring contracted guanidine derived five-membered C,N] palladacycle, (C,N)PdBr(C NXy)] (6) were prepared in high yield following the established methods with a view aimed at understanding the influence of the substituents on the aryl rings of the guanidine upon the solid state structure and solution behaviour of palladacycles. Palladacycles were characterised by microanalytical, IR, NMR and mass spectral data. The molecular structures of 1a, 1c, 2a, 2b, 3a, 3c, 3d, and 4-6 were determined by single crystal X-ray diffraction data. Palladacycles 1a and 1c were shown to exist as a dimer in transoid in-in conformation in the solid state but as a mixture of a dimer in major proportion and a monomer (kappa(2)-O,O'-OAc) in solution as deduced from H-1 NMR data. Palladacycles 2a and 2b were shown to exist as a dimer in transoid conformation in the solid state but the former was shown to exist as a mixture of a dimer and presumably a trimer in solution as revealed by a variable temperature H-1 NMR data in conjunction with ESI-MS data. The cis configuration around the palladium atom in 3a, 3c, and 3d was ascribed to steric influence of the aryl moiety of =NAr unit and that in 4-6 was ascribed to antisymbiosis. The solution behaviour of 3d was studied by a variable concentration (VC) H-1 NMR data.

Human la protein interaction with GCAC near the initiator AUG enhances hepatitis C virus RNA replication by promoting linkage between 5 ` and 3 ` untranslated regions

Human La protein has been implicated in facilitating the internal initiation of translation as well as replication of hepatitis C virus (HCV) RNA. Previously, we demonstrated that La interacts with the HCV internal ribosome entry site (IRES) around the GCAC motif near the initiator AUG within stem-loop IV by its RNA recognition motif (RRM) (residues 112 to 184) and influences HCV translation. In this study, we have deciphered the role of this interaction in HCV replication in a hepatocellular carcinoma cell culture system. We incorporated mutation of the GCAC motif in an HCV monocistronic subgenomic replicon and a pJFH1 construct which altered the binding of La and checked HCV RNA replication by reverse transcriptase PCR (RT-PCR). The mutation drastically affected HCV replication. Furthermore, to address whether the decrease in replication is a consequence of translation inhibition or not, we incorporated the same mutation into a bicistronic replicon and observed a substantial decrease in HCV RNA levels. Interestingly, La overexpression rescued this inhibition of replication. More importantly, we observed that the mutation reduced the association between La and NS5B. The effect of the GCAC mutation on the translation-to-replication switch, which is regulated by the interplay between NS3 and La, was further investigated. Additionally, our analyses of point mutations in the GCAC motif revealed distinct roles of each nucleotide in HCV replication and translation. Finally, we showed that a specific interaction of the GCAC motif with human La protein is crucial for linking 5' and 3' ends of the HCV genome. Taken together, our results demonstrate the mechanism of regulation of HCV replication by interaction of the cis-acting element GCAC within the HCV IRES with human La protein.

Crystal structures and binding studies of atovaquone and its derivatives with cytochrome bc(1): a molecular basis for drug design

Crystal structure of trans-atovaquone (antimalarial drug), its polymorph and its stereoisomer (cis) along with five other derivatives with different functional groups have been analyzed. Based on the conformational features of these compounds and the characteristics of the nature of intermolecular interactions, valuable insights into the atomistic details of protein-inhibitor interactions have been derived by docking studies. Atovaquone and its derivatives pack in the crystal lattice using intermolecular O-H center dot center dot center dot O hydrogen bond dimer motifs supported by surrogate weak interactions including C-H center dot center dot center dot O and C-H center dot center dot center dot Cl hydrogen bonds. The docking results of these molecules with cytochrome bc(1) show preferences to form N-H center dot center dot center dot O, O-H center dot center dot center dot O and O-H center dot center dot center dot Cl hydrogen bonds. The involvement of halogen atoms in the binding pocket appears to be significant and is contrary to the theoretically predicted mechanism of protein-ligand docking reported earlier based on mimicking experimental binding results of stigmatellin with cytochrome bc(1). The significance of subtle energy factors controlled by weak intermolecular interactions appears to play a major role in drug binding.

Investigating proline puckering states in diproline segments in proteins

In the current study, the puckering states of the Proline ring occurring in diproline segments (LPro-LPro) in proteins has been investigated with a segregation made on the basis of cis and trans states for the Pro-Pro peptide bond and the conformational states for the diproline segment to investigate the effects of conformation of the diproline segment on the corresponding puckering state of the Proline ring in the segment if any. The value of the endocyclic ring torsional angles of the pyrrolidine ring has been used for calculating and visualizing various puckering states using a proposed new sign convention (+/-) nomenclature. The results have been compared to that obtained in a previous study on peptides from this group. In this study, quite interestingly, the Planar (G) conformation that was present in 14.3% of the cases in peptides, appears to be nearly a rare conformation in the case of proteins (1.9%). The present study indicates that the (C-exo/C-exo), (C-exo/Twisted C-exo-C-endo) and (Twisted C-endo-C-exo/Twisted C-endo-C-exo) categories are the most preferred combinations. For Proline rings in proteins, the states C-exo, Twisted C-exo-C-endo and Twisted C-endo-C-exo are the most preferred states. Within diproline segments, the pyrrolidine ring conformations do not show a strong co-relation to the backbone conformation in which they are observed. It is likely that five-membered rings have a considerable plasticity of structure and are readily deformed to accommodate a variety of energetically preferred backbone conformations.

Splicing Functions and Global Dependency on Fission Yeast Slu7 Reveal Diversity in Spliceosome Assembly

The multiple short introns in Schizosaccharomyces pombe genes with degenerate cis sequences and atypically positioned polypyrimidine tracts make an interesting model to investigate canonical and alternative roles for conserved splicing factors. Here we report functions and interactions of the S. pombe slu7(+) (spslu7(+)) gene product, known from Saccharomyces cerevisiae and human in vitro reactions to assemble into spliceosomes after the first catalytic reaction and to dictate 3' splice site choice during the second reaction. By using a missense mutant of this essential S. pombe factor, we detected a range of global splicing derangements that were validated in assays for the splicing status of diverse candidate introns. We ascribe widespread, intron-specific SpSlu7 functions and have deduced several features, including the branch nucleotide-to-3' splice site distance, intron length, and the impact of its A/U content at the 5' end on the intron's dependence on SpSlu7. The data imply dynamic substrate-splicing factor relationships in multiintron transcripts. Interestingly, the unexpected early splicing arrest in spslu7-2 revealed a role before catalysis. We detected a salt-stable association with U5 snRNP and observed genetic interactions with spprp1(+), a homolog of human U5-102k factor. These observations together point to an altered recruitment and dependence on SpSlu7, suggesting its role in facilitating transitions that promote catalysis, and highlight the diversity in spliceosome assembly.