Conformational studies on beta-bend containing a cis peptide unit

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds - either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C(gamma)-endo and C(gamma)-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.

Membranes of Cationic Gemini Lipids based on Cholesterol with Hydroxyl Headgroups and their Interactions with DNA and Phospholipid

Two series of cholesterol-based cationic gemini lipids with and without hydroxyl functions at the headgroups possessing different lengths of polymethylene -(CH2)(n)-] (n = 3, 4, 5, 6, 12) spacer have been synthesized. Each gemini lipid formed stable suspension in water. The suspensions of these gemini lipids in water were investigated using transmission electron microscopy, dynamic light scattering, zeta potential measurements and X-ray diffraction to characterize the nature of the individual aggregates formed therein. The aggregation properties of these gemini lipids in water were found to strongly depend upon the length of the spacer and the presence of hydroxyl group at the headgroup region. Lipoplex formation (DNA binding) and the release of the DNA from such lipoplexes were performed to understand the nature of interactions that prevail between these cationic cholesterol aggregates and duplex DNA. The interactions between such gemini lipids and DNA depend both on the presence of OH on the headgroups and the spacer length between the headgroups. Finally, we studied the effect of incorporation of each cationic gemini lipid into dipalmitoyl phosphatidylcholine vesicles using differential scanning calorimetry. The properties of the resulting mixed membranes were found again to depend upon the nature of the headgroup and the spacer chain length.

Self-assembly of neutral and cationic Pd-II organometallic molecular rectangles: synthesis, characterization and nitroaromatic sensing

Design and synthesis of three novel 2 + 2] self-assembled molecular rectangles 1-3 via coordination driven self-assembly of predesigned Pd(II) ligands is reported. 1,8-Diethynylanthracene was assembled with trans-Pd(PEt3)(2)Cl-2 in the presence of CuCl catalyst to yield a neutral rectangle 1 via Pd-C bond formation. Complex 1 represents the first example of a neutral molecular rectangle obtained via C-Pd coordination driven self-assembly. A new Pd-2(II) organometallic building block with 180 degrees bite-angle 1,4-bistrans-(ethynyl)Pd(PEt3)(2)(NO3)] benzene (M-2) containing ethynyl functionality was synthesized in reasonable yield by employing Sonagashira coupling reaction. Self-assembly of M-2 with two organic clip-type donors (L-2-L-3) afforded 2 + 2] self-assembled molecular rectangles 2 and 3, respectively L-2 = 1,8-bis(4-pyridylethynyl) anthracene; L-3 = 1,3-bis(3-pyridyl) isophthalamide]. The macrocycles 1-3 were fully characterized by multinuclear NMR and ESI-MS spectroscopic techniques, and in case of 1 the structure was unambiguously determined by single crystal X-ray diffraction analysis. Incorporation of Pd-ethynyl bonds helped to make the assemblies p-electron rich and fluorescent in nature. Complexes 1-2 showed quenching of fluorescence intensity in solution in presence of nitroaromatics, which are the chemical signatures of many commercially available explosives.

Dialkylaminopyridine catalysed esterolysis of p-nitrophenyl alkanoates in different cationic microemulsions

The reactions of p-nitrophenyl alkanoate esters with dialkylaminopyridine (DAAP) and its related mono- and di-anionic water-soluble derivatives have been studied separately in three different microemulsion (ME) media. These were (a) oil-in-water ME (O/W), (b) water-in-oil ME (W/O) and (c) a bicontinuous ME, where oil and water are in nearly comparable amounts. All the ME systems were stabilized by cationic surfactant, cetyltrimethylammonium bromide (CTABr) and butanol as a cosurfactant. The second-order rate constants (k(2)) in the microemulsion media were also determined : over a phase volume (phi) of approximately 0.13-0.46. In order to explain the contribution of effective concentration of the nucleophiles in the aqueous pseudophase, corrected rate constants k(2 phi) = k(2)(1 - phi) were obtained, The rate constants of the corresponding hydrolytic reactions were also examined in CTABr micelles. While the DAAP catalysts were partitioned between the micellar and aqueous pseudophases in ME, the hydrophobic substrates were found to be mainly confined to oil-rich phases, Present results indicate that the main effect of ME media on the hydrolysis reaction is due,to both electrostatic reasons and substrate partitioning.

Identification of the active-site peptide of 2,3-dihydroxybenzoic acid decarboxylase from Aspergillus oryzae

The non-oxidative decarboxylation of aromatic acids is a poorly understood reaction. The transformation of 2,3-dihydroxybenzoic acid to catechol in the fungal metabolism of indole is a prototype of such a reaction. 2,3-Dihydroxybenzoic acid decarboxylase (EC 4.1.1.46) which catalyzes this reaction was purified to homogeneity from anthranilate induced cultures of Aspergillus oryzae using affinity chromatography. The enzyme did not require cofactors like NAD(+), PLP, TPP or metal ions for its activity. There was no spectral evidence for the presence of enzyme bound cofactors. The preparation, which was adjudged homogeneous by the criteria of SDS-PAGE, sedimentation analysis and N-terminal analysis, was characterized for its physicochemical and kinetic parameters. The enzyme was inactivated by group-specific modifiers like diethyl pyrocarbonate (DEPC) and N-ethylmaleimide (NEM). The kinetics of inactivation by DEPC suggested the presence of a single class of essential histidine residues, the second order rate constant of inactivation for which was 12.5 M(-1) min(-1). A single class of cysteine residues was modified by NEM with a second order rate constant of 33 M(-1) min(-1). Substrate analogues protected the enzyme against inactivation by both DEPC and NEM, suggesting the Location of the essential histidine and cysteine to be at the active site of the enzyme. The incorporation of radiolabelled NEM in a differential labelling experiment was 0.73 mol per mol subunit confirming the presence of a single essential cysteine per active-site. Differentially labelled enzyme was enzymatically cleaved and the peptide bearing the label was purified and sequenced. The active-site peptide LLGLAETCK and the N-terminal sequence MLGKIALEEAFALPRFEEKT did not bear any similarity to sequences reported in the Swiss-Prot Protein Sequence Databank, a reflection probably of the unique primary structure of this novel enzyme. The sequences reported in this study will appear in the Swiss-Prot Protein Sequence Databank under the accession number P80402.

Crystal and molecular structure of Boc-Phe-Val-OMe; comparison of the peptide conformation with its dehydro analogue

The crystal structure of the peptide Boc-Phe-Val-OMe determined by X-ray diffraction methods is reported in this paper. The crystals grown from aqueous methanol are orthorhombic, space group P2(1)2(1)2(1), a = 11.843(2), b = 21.493(4), c = 26.676(4)Angstrom and V = 6790 Angstrom(3). Data were collected on a CAD4 diffractometer using MoK2 radiation (lambda = 0.7107 Angstrom) up to Bragg angle theta = 26 degrees. The structure was solved by direct methods and refined by a least-squares procedure to an R value of 6.8% for 3288 observed reflections. There are three crystallographically independent peptide molecules in the asymmetric unit. All the three molecules exhibit extended conformation. The sidechain of the Val(2) residue shows two different conformations. The conformation of the peptide Boc-Phe-Val-OMe is compared with the conformation of Ac-Delta Phe-Val-OH. It is observed that while Boc-Phe-Val-OMe exhibits an extended conformation, Ac-Delta Phe-Val-OH shows a folded conformation. The results of this comparison highlight the conformation constraining property of the Delta Phe residue. Interestingly, even though Boc-Phe-Val-OMe and Ac-Delta Phe-Val-OH are conformationally different, they exhibit similar packing patterns in the solid state. (C) Munksgaard 1995.

Synthesis, redox and electrochemical properties of new anthraquinone-attached micelle- and vesicle-forming cationic amphiphiles

Three new cationic amphiphiles bearing anthraquinone moieties at the polar headgroup region were synthesized, The single-chain amphiphile, N,N-dimethyl-N-octadecyl-N-(9,10-dihydro dioxoanthracen-2-ylmethyl)ammonium bromide 1, in the presence of cetyltrimethylammonium bromide upon dispersion in water gave co-micellar aggregates containing covalently attached anthraquinone residues at the polar aqueous interfaces. The other two double-chain amphiphiles, N,N-dioctadecyl-N-methyl-N-(9,10-dihydro-9,10-dioxoanthracen-2-ylmethyl)ammonium bromide 2 and N,N-dimethyl-N-(1,2-bispalmitoyloxypropanyl)-N-(9,10-dihydro-9,10-dioxanthracen-2-ylmethyl)ammonium bromide 3, however, on dispersion in aqueous media produced vesicular aggregates. The critical temperatures for the gel to liquid-crystalline-like phase transition processes for the vesicular systems were determined by following temperature-dependent changes in the ratios of keto-enol tautomeric forms of benzoylacetanilide doped within respective. vesicular assemblies. The redox chemistry of the these supramolecular assemblies was also studied by following the time-dependent changes in the ITV-VIS absorption spectroscopy in the presence of exogenous reducing or oxidizing agents, Electrochemical studies using glassy carbon electrodes reveal that redox-active amphiphiles adsorb on to the glassy carbon surfaces to form electroactive deposits when dipped into aqueous suspensions of either of these aggregates irrespective of the micellar or vesicular nature of the dispersions.

Impact of metal binding on the antitumor activity and cellular imaging of a metal chelator cationic imidazopyridine derivative

A new water soluble cationic imidazopyridine species, viz. (1E)-1-((pyridin-2-yl)methyleneamino)-3-(3(pyridin-2-yl) imidazo1,5-a]pyridin-2(3H)-yl)propan-2-ol (1), as a metal chelator is prepared as its PF6 salt and characterized. Compound 1 shows fluorescence at 438 nm on excitation at 342 nm in Tris-HCl buffer giving a fluorescence quantum yield (phi) of 0.105 and a life-time of 5.4 ns. Compound 1, as an avid DNA minor groove binder, shows pUC19 DNA cleavage activity in UV-A light of 365 nm forming singlet oxygen species in a type-II pathway. The photonuclease potential of 1 gets enhanced in the presence of Fe2+, Cu2+ or Zn2+. Compound 1 itself displays anticancer activity in HeLa, HepG2 and Jurkat cells with an enhancement on addition of the metal ions. Photodynamic effect of 1 at 365 nm also gets enhanced in the presence of Fe2+ and Zn2+. Fluorescence-based cell cycle analysis shows a significant dead cell population in the sub-G1 phase of the cell cycle suggesting apoptosis via ROS generation. A significant change in the nuclear morphology is observed from Hoechst 33258 and an acridine orange/ethidium bromide (AO/EB) dual nuclear staining suggesting apoptosis in cells when treated with 1 alone or in the presence of the metal ions. Apoptosis is found to be caspase-dependent. Fluorescence imaging to monitor the distribution of 1 in cells shows that 1 in the presence of metal ions accumulates predominantly in the cytoplasm. Enhanced uptake of 1 into the cells within 12 h is observed in the presence of Fe2+ and Zn2+.

Observation of Water-Mediated Helix-Terminating Conformation in a Dehydrophenylalanine Peptide: Crystal and Solution Structure of the Octapeptide Ac-.DELTA.Phe-Val-.DELTA.Phe-Phe-Ala-Val-.DELTA.Phe-Gly-OMe

We have synthesised and determined the solution conformation and X-ray crystal structure of the octapeptide Ac-Delta Phe(1)-Val(2)-Delta Phe(3)-Phe(4)-Ala(5)-Val(6)-Delta Phe(7)-Gly(8)-OCH3 (Delta Phe = alpha,beta-dehydrophenylalanine) containing three Delta Phe residues as conformation constraining residues. In the solid state, the peptide folds into (i) an N-terminal (3)10(R)-helical pentapeptide segment, (ii) a middle non-helical segment, and (iii) a C-terminal incipient (3)10(L)-helical segment. The results of H-1 NMR data also suggest that a similar multiple-turn conformation for the peptide is largely maintained in solution. Though the C-terminal helix is incipient, the overall conformation of the octapeptide matches well with the conformation of the hairpins reported. Comparison of the pi-turn seen in the octapeptide molecule with those observed in proteins at the C-terminal end of helixes shows the structural similarity among them. A water molecule mediates the 5 --> 2 hydrogen bond in the pi-turn region. This is the first example of a water-inserted pi-turn in oligopeptides reported so far. Comparison between the present octapeptide and another (3)10(R)-helical dehydro nonapeptide Boc-Val-Delta Phe-Phe-Ala-Phe-Delta Phe-Val-Delta Phe-Gly-OCH3 solved by us recently, demonstrates the possible sequence-dependent conformational variations in alpha,beta-dehydrophenylalanine-containing oligopeptides.

Synthesis and Antioxidant Activity of Peptide-Based Ebselen Analogues

A series of di- and tripeptide-based ebselen analogues has been synthesized. The compounds were characterized by H-1, C-13, and Se-77 NMR spectroscopy and mass spectral techniques. The glutathione peroxidase (GPx)-like antioxidant activity has been studied by using H2O2, tert-butyl hydroperoxide (tBuOOH), and cumene hydroperoxide (Cum-OOH) as substrates, and glutathione (GSH) as a co-substrate. Although all the peptide-based compounds have a selenazole ring similar to that of ebselen, the GPx activity of these compounds highly depends on the nature of the peptide moiety attached to the nitrogen atom of the selenazole ring. It was observed that the introduction of a phenylalanine (Phe) amino acid residue in the N-terminal reduces the activity in all three peroxide systems. On the other hand, the introduction of aliphatic amino acid residues such as valine (Val) significantly enhances the GPx activity of the ebselen analogues. The difference in the catalytic activity of dipeptide-based ebselen derivatives can be ascribed mainly to the change in the reactivity of these compounds toward GSH and peroxide. Although the presence of the Val-Ala-CO2Me moiety facilitates the formation of a catalytically active selenol species, the reaction of ebselen analogues that has a Phe-Ile-CO2Me residue with GSH does not generate the corresponding selenol. To understand the antioxidant activity of the peptide-based ebselen analogues in the absence of GSH, these compounds were studied for their ability to inhibit peroxynitrite (PN)-mediated nitration of bovine serum albumin (BSA) and oxidation of dihydrorhodamine 123. In contrast to the GPx activity, the PN-scavenging activity of the Phe-based peptide analogues was found to be comparable to that of the Val-based compounds. However, the introduction of an additional Phe residue to the ebselen analogue that had a Val-Ala dipeptide significantly reduced the potency of the parent compound in PN-mediated nitration.

Synthesis, Thermotropic Behavior, and Permeability Properties of Vesicular Membranes Composed of Cationic Mixed-Chain Surfactants

In order to elucidate the role of the linkage region that connects polar headgroups with hydrophobic segments in a lipid monomer, cationic mixed-chain amphiphiles containing acyl and alkyl hydrophobic segments connected at the level of Me(2)N(+) headgroups 2a-d were synthesized. Related dialkyldimethyl-ammonium ion surfactants 1a-e and diacyl systems 3a-c were also synthesized. Despite mismatch in the connector region, amphiphiles 2a-d form bilayer vesicles like their dialkyl and diacyl counterparts, as revealed by electron microscopy. Introduction of an ester connector function between the polar and hydrophobic parts raises the phase transition temperature (T-m), transition enthalpies, and resistance to ion permeation. Consideration of energy minimized conformations points toward the importance of differences in the depth of chain penetration into the putative bilayer.

Crystal structure of Boc-LAla-Delta Phe-Delta Phe-Delta Phe-Delta Phe-NHMe: a left-handed helical peptide

alpha,beta-Dehydrophenylalanine residues constrain the peptide backbone to beta-bend conformation. A pentapeptide containing four consecutive (Delta Phe) residues has been synthesised and crystallised. The peptide Boc-LAla-Delta Phe-Delta Phe-Delta Phe-Delta Phe-NHMe (C45H46N6O7, MW = 782.86) was crystallised from an acetonitrile/methanol mixture. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1) With a = 19.455(6), b = 20.912(9), c = 11.455(4) Angstrom and Z = 4. The X-ray (MoKalpha, lambda = 0.7107 Angstrom) intensity data were collected using the Rigaku-AFC7 diffractrometer. The crystal structure was determined by direct methods and refined using the least-squares technique, R = 8.41% for 1827 reflections with \F-o\ > 4 sigma\F-o\. The molecule contains the largest stretch of consecutive dehydrophenylalanine residues whose crystal structure has been determined so far. The peptide adopts left-handed 3(10)-helical conformation despite the presence of LAla at the N-terminus. The mean phi, psi values, averaged across the last four residues are 56.8 degrees and 17.5 degrees, respectively. There are four 4-->1 intramolecular hydrogen bonds, characteristic of the 3(10)-helix. In the crystal each molecule interacts with four crystallographically symmetric molecules with one hydrogen bond each.

DNA binding properties of some cationic acridine derivatives

Four cationic acridine derivatives have been synthesized. The positively charged amine residue in one of these is connected directly on to the acridine nucleus and in three other acridines, the amines are connected via a 9-CH2 unit to acridine. We have investigated the binding of these acridines with mammalian DNA by absorption titration, UV- and induced-CD spectroscopy and competitive ethidium bromide displacement fluorescence assay. The effects on the DNA duplex denaturation melting temperatures upon binding of each one of these are also examined. The results obtained herein clearly show that the introduction of a -CH2 group in the im mediate vicinity of the interrelation moiety introduces alterations in the DNA binding characteristics of the resulting acridines.

Microwave Assisted Synthesis and Antimicrobial Study of Schiff Base Vanadium(IV) Complexes of Phenyl Esters of Amino Acids

Schiff base vanadium(IV) complexes of phenyl esters of the two acidic amino acids, i.e., aspartic and glutamic acid, were synthesized. The phenyl esters of these amino acids were synthesized by conventional method whereas the Schiff base vanadium(IV) complexes were synthesized using microwave irradiation. The complexes were characterized by spectroscopic tools such as IR, 1H NMR, mass (ES), ESR, and UV visible spectroscopy. All the complexes were studied for antibacterial and antifungal activity and found to be moderately active.