Oligomerization of N-Tosylindole with Aluminum Chloride

The reactivity of N-tosylindole (4) in the presence of aluminum chloride was studied, and two types of oligomerization of 4 were observed. One type was condensation between both pyrrole parts (dimers 5 and 6 and trimer 7) and the other was between a pyrrole part and a benzene part of each indole nucleus (dimers 8 and 9).     

Netropsin and bis-netropsin analogs as inhibitors of the catalytic activity of mammalian DNA topoisomerase II and topoisomerase cleavable complexes.

This study examined the ability of netropsin and related minor groove binders to interfere with the actions of DNA topoisomerases II and I. We evaluated a series of netropsin dimers linked with flexible aliphatic chains of different lengths. These agents are potentially able to occupy longer stretches of DNA than the parental drug as a result of bidentate binding. Both netropsin and its dimers were found: (i) to inhibit the catalytic activity of isolated topoisomerase II and (ii) to interfere with the stabilization of the cleavable complexes of topoisomerase II and I in nuclei. Dimers with linkers consisting of 0-4 and 6-9 methylene groups (n) were far more inhibitory than netropsin against isolated enzyme and in the nuclear system. The compound with n = 5 was less active than netropsin in both assays while the dimer with n = 10 inhibited only the isolated enzyme. The comparison of dimers with fixed linker length (n = 2) but varying number of N-methylpyrrole residues (from 1 to 3) revealed that the inhibitory properties were enhanced with increasing number of N-methylpyrrole units. For dimers with varying linker length, drug ability to inhibit catalytic activity of isolated topoisomerase II was positively correlated with calf thymus DNA association constants. In contrast, no such correlation existed in nuclei. However, the inhibitory effects in the nuclear system were correlated with the association constants for poly(dAdT). The results indicate that bidentate binding can significantly enhance anti-topoisomerase activity of netropsin related dimeric minor groove binders. However, other factors such as the length of the linker, the number of pyrrole moieties and the nature of the target (isolated enzyme/DNA versus chromatin in nuclei) also contribute to these activities.     

Structural effects of DNA sequence on T.A recognition by hydroxypyrrole/pyrrole pairs in the minor groove

Synthetic polyamides composed of three types of aromatic amino acids, N-methylimidazole (Im), N-methylpyrrole (Py) and N-methyl-3-hydroxypyrrole (Hp) bind specific DNA sequences as antiparallel dimers in the minor groove. The side-by-side pairings of aromatic rings in the dimer afford a general recognition code that allows all four base-pairs to be distinguished. To examine the structural consequences of changing the DNA sequence context on T.A recognition by Hp/Py pairs in the minor groove, crystal structures of polyamide dimers (ImPyHpPy)(2) and the pyrrole counterpart (ImPyPyPy)(2) bound to the six base-pair target site 5'-AGATCT-3' in a ten base-pair oligonucleotide have been determined to a resolution of 2.27 and 2.15 A, respectively. The structures demonstrate that the principles of Hp/Py recognition of T.A are consistent between different sequence contexts. However, a general structural explanation for the non-additive reduction in binding affinity due to introduction of the hydroxyl group is less clear. Comparison with other polyamide-DNA cocrystal structures reveals structural themes and differences that may relate to sequence preference.     

Modeling the weak hydrogen bonding of pyrrole and dichloromethane through Raman and DFT study

Raman spectra of neat pyrrole (C(4)H(5)N) and its binary mixtures with dichloromethane (CH(2)Cl(2), DCM) with varying mole fractions of C(4)H(5)N from 0.1 to 0.9 were recorded in order to monitor the influence of molecular interaction on spectral features of selected vibrational bands of pyrrole in the region 600-1600 cm(-1). Only 1369 cm(-1) vibrational band of pyrrole shows a significant change in its peak position in going from neat pyrrole to the complexes. The 1369 cm(-1) band shows (～6 cm(-1)) blue shift upon dilution and the corresponding linewidth shows the maximum shift at C?=?0.5 mole fraction of pyrrole upon dilution which clearly indicates that the concentration fluctuation model plays major role. Quantum chemical calculation using density functional theory (DFT) and ab-initio (MP2 and HF) methods were performed employing high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat pyrrole and its complexes with DCM in gas phase. Basis set superimpose error (BSSE) correction was also introduced by using the counterpoise method. In order to account for the solvent effect on vibrational features and changes in optimized structural parameters of pyrrole, polarizable continuum model (PCM) (bulk solvations) and PCM (specific plus bulk solvations) calculations were performed. Two possible configurations of pyrrole + DCM complex have been predicted by B3LYP and HF methods, whereas the MP2 method gave only single configuration in which H atom of DCM is bonded to π ring of the pyrrole molecule. This affects significantly the ring vibrations of pyrrole molecule, which was also observed in our experimental results.     

In vitro multimerization of von Willebrand factor is triggered by low pH. Importance of the propolypeptide and free sulfhydryls

Large von Willebrand factor (vWf) multimers are assembled by the formation of disulfide bonds between dimers in trans Golgi and post-Golgi compartments. We were able to reproduce this process in a cell-free system using purified vWf dimers. The multimers formed in vitro extended to 5 x 10(6) Da and were similar in size distribution to those secreted constitutively by endothelial cells in culture. Multimerization occurred only at acidic pH with an optimum at pH 5.8 and needed the continued presence of an acidic pH for it to proceed. Pro-vWf dimers multimerized, whereas mature dimers failed to assemble into large multimers. Multimerization required the propolypeptide to be a contiguous part of pro-vWf subunits since free propolypeptide did not promote multimerization of mature dimers. In addition, multimers formed in the presence of both pro-vWf and mature vWf dimers incorporated only pro-vWf dimers. Two out of six available monoclonal antibodies to the prosequence inhibited multimerization. Multimerization was also inhibited by chemical blocking of free sulfhydryl(s). The free sulfhydryl(s) were localized to the mature region of the pro-vWf by examination of the mature subunit and the propolypeptide derived by proteolytic cleavage of pro-vWf subunits.     

Hepatoprotective pyrrole derivatives of Lycium chinense fruits

As a part of our search for hepatoprotective compounds from Lycium chinense fruits, three new pyrrole derivatives (1-3) were isolated. These compounds and a related synthetic methylated compound (4) were evaluated for their biological activity and structure-activity relationship, and compounds 1 and 2 showed hepatoprotective effects comparable to silybin at the concentration of 0.1 microM (64.4 and 65.8%, respectively).     

Genetic analysis of the biosynthesis of the pyrrole and carbamoyl moieties of coumermycin A1 and novobiocin

The aminocoumarin antibiotic coumermycin A(1) contains a central and two terminal pyrrole moieties. The coumermycin gene cluster in Streptomyces rishiriensis contains three genes (couN3, couN4 and couN5) that show sequence similarity to genes involved in the biosynthesis of the pyrrole moieties of pyoluteorin in Pseudomonas fluorescens and of undecylprodiginine in S. coelicolor. The gene couN3, which codes for a putative L-prolyl-S-PCP dehydrogenase, and the gene couN4, which encodes a putative L-prolyl-AMP ligase, were disrupted using in-frame deletion and insertional inactivation, respectively. HPLC analysis of culture extracts showed that formation of the two terminal pyrrole moieties was abolished in the couN3 (-) und couN4 (-) mutants. The mutants accumulated coumermycin D, which contains only the central pyrrole moiety. This result not only confirmed the involvement of couN3 and couN4 in the biosynthesis of the terminal pyrrole-2-carboxylic acid moieties of coumermycin A(1), but also indicated, for the first time, that the central 3-methylpyrrole-2,4-dicarboxylic acid unit of the coumermycins is formed by a biosynthetic pathway that differs from that used to assemble the terminal pyrrole moieties. novN, a putative carbamoyl transferase gene from the gene cluster for novobiocin biosynthesis in S. spheroides was expressed in the couN3 (-) mutant. This led to the formation of bis-carbamoylated coumermycin D, a novel compound of the coumermycin series.     

Computational evaluation of intermolecular interactions of a universal base 3-nitropyrrole in stacked dimers and DNA duplexes

The stacking interactions between a universal base of 3-nitropyrrole (3NP) and four canonical nucleobases were studied by means of ab initio molecular orbital calculations. The stabilities of the complexes are comparable to those of the stacked dimers of canonical bases reported previously. The detailed analysis of the interaction energies revealed the importance of the dipole-dipole interaction included in the Hartree-Fock terms to determine the geometry dependence of the stacking energies. It was also clarified that the dispersion energies included in the electron-correlation terms were essential to obtain adequate stabilities. The contribution of the nitro group was evaluated by the comparative studies of pyrrole and 3NP. The increased molecular dipole moment and surface are expected to account for the enhancement of the stability of the stacked dimers containing 3NP. The force field parameters required for calculation of the molecular mechanics of 3NP were obtained for 3NP on the basis of these molecular orbital calculations. The energy-minimized structures obtained by the molecular mechanics calculations of 3NP accorded with those obtained by the molecular orbital calculations described above. A DNA duplex structure containing 3NP-A, 3NP-T, or 3NP-C was calculated by use of these force field parameters. In the case of 3NP-A, the computationally calculated structure was in good agreement with that previously determined by use of (1)H-NMR except for the orientation of the nitro group.     

Transient electric birefringence of human erythroid spectrin dimers and tetramers at ionic strengths of 4 mm and 53 mm

In conventional electrooptic studies the sample ionic strength must for technical reasons be kept below about 3 mm, which is only 2% of the ionic strength at physiological conditions. In particular for flexible polyelectrolytic macromolecules it can in general not be ruled out that both the conformational average and dynamics at ionic strength 3 mm and below may differ significantly from what it is at physiological conditions. Here we report on the first electrooptic study of human erythroid spectrin dimers and tetramers at ionic strengths higher than 3 mm. All measurements in this study were carried out at both ionic strength 4 mm (2.5 mm HEPES + 1 mm NaCl) and 53 mm (2.5 mm HEPES + 50 mm NaCl). Spectrin tetramers were studied only at 4°C whereas the dimers were studied at both 4 °C and 37°C. At 4°C there is a striking quantitative similarity between the transient electric birefringence (TEB) of spectrin dimers and tetramers. Also, the TEB of spectrin dimers at 37°C was very similar to the results at 4°C. The contour length and the molecular weight of spectrin dimers and tetramers are known. The dominating TEB relaxation time is in all cases only a fraction of what is predicted theoretically if the spectrin dimers and tetramers are assumed to be stiff and extended molecules. In sum, the new TEB data constitute strong electrooptic evidence confirming that spectrin dimers and tetramers have a highly flexible structure, and demonstrate for the first time that a major part of the intrachain dynamics of the spectrin is quite insensitive to an increase of the ionic strength from 4 mm to 53 mm. Use of the reversing electric field pulse technique for all conditions studied yields TEB data suggesting that the orientation of both spectrin dimers and tetramers in an electric field is dominated by a permanent rather than an induced electric dipole moment. Received: 26 August 1998 / Revised version: 8 February 1999 / Accepted: 11 February 1999     

Reaction of dihydropyrrolizines with deoxyribonucleic acids in vitro

1. Thermal denaturation profiles of Escherichia coli DNA pretreated with monocrotaline pyrrole in vitro showed no difference from control DNA samples during heating. A substantial increase in the degree of renaturation during cooling of the pretreated DNA samples was observed. The degree of renaturation was dependent on the concentration of pyrrole used. 2. When rat liver DNA was pretreated with monocrotaline pyrrole there was a greater degree of renaturation after heat treatment than was found with E. coli DNA. 3. Equilibrium-density-gradient centrifugation in alkaline caesium chloride showed that DNA pretreated with monocrotaline pyrrole and heat denatured, renatured to a greater extent on quenching in ice than did untreated control DNA. The degree of renaturation was similar whether the initial treatment of the DNA with pyrrole was for 1 or for 15min. The reaction also appeared to be independent of pH between 5.5 and 9.0. 4. Retrorsine pyrrole was as effective as monocrotaline pyrrole in cross-linking the DNA, but monocrotaline pyrrole exposed to water for 5min before the addition of the DNA was ineffective. Pretreatment of E. coli DNA with synthetic bis-hydroxymethylpyrrole esters also caused renaturation after heat treatment. Monoesters were ineffective. 5. After treatment of rats with retrorsine, no cross-linking of the liver DNA could be demonstrated.     

New strapped calix[4]pyrrole based receptor for anions

Calix[4]pyrrole bearing catechol-derived diether strap linked via alkyl chains has been synthesized and characterized for the first time. The strap with 1,2-diether link is providing a relatively constrained geometry on its side of the calix[4]pyrrole moiety. As a result only one isomer (cis-type) of the receptor formed during reaction. The crystal structure reveals two molecules of methanol bound to the host. This calix[4]pyrrole also exhibits enhanced binding towards halide anions compared to simple calix[4]pyrrole apart from showing binding towards dihydrogenphosphate and acetate ions. The association constants are quite similar to that found for orcinol strapped calix[4]pyrrole towards halide anions in general, but having a higher preference for chloride than bromide ion in particular. Further it shows very strong preference towards fluoride ion.     

Synthesis of Lipid Derivatives of Pyrrole Polyamide and Their Biological Activity

Novel fatty acyl and phospholipid derivatives of pyrrole polyamide were synthesized. Their cytotoxicity against a cancer cell line of MT-4 cells and those infected by human immunodeficiency virus (HIV) was examined. Although no anti-HIV activity was found, their cytotoxicitty against the cancer cells was significantly enhanced by introducing a lipophilic group into the pyrrole polyamide.     

Synthesis of lipid derivatives of pyrrole polyamide and their biological activity

Novel fatty acyl and phospholipid derivatives of pyrrole polyamide were synthesized. Their cytotoxicity against a cancer cell line of MT-4 cells and those infected by human immunodeficiency virus (HIV) was examined. Although no anti-HIV activity was found, their cytotoxicitty against the cancer cells was significantly enhanced by introducing a lipophilic group into the pyrrole polyamide.     

Enzymatic syntheses of 6-(4H-selenolo[3,2-b]pyrrolyl)-L-alanine, 4-(6H-selenolo[2,3-b]pyrrolyl)-L-alanine, and 6-(4H-furo[3,2-b]pyrrolyl-L-alanine

6-(4H-Selenolo[3,2-b]pyrrolyl)-L-alanine 1, 4-(6H-selenolo[2,3-b]pyrrolyl)-L-alanine 2, and 6-(4H-furo[3,2-b]pyrrolyl)-L-alanine 3 have been synthesized via reactions of selenolo[3,2-b]pyrrole, selenolo[2,3-b]pyrrole, and furo[3,2-b]pyrrole, respectively, with L-serine. The reactions are catalyzed by Salmonella typhimurium tryptophan synthase.     

Structural characterization of pyrrolic cross-links in collagen using a biotinylated Ehrlich's reagent

The structures of pyrrolic forms of cross-links in collagen have been confirmed by reacting collagen peptides with a biotinylated Ehrlich's reagent. This reagent was synthesized by converting the cyano group of N-methyl-N-cyanoethyl-4-aminobenzaldehyde to a carboxylic acid, followed by conjugation with biotin pentyl-amine. Derivatization of peptides from bone collagen both stabilized the pyrroles and facilitated selective isolation of the pyrrole-containing peptides using a monomeric avidin column. Reactivity of the biotinylated reagent with collagen peptides was similar to that of the standard Ehrlich reagent, but heat denaturation of the tissue before enzyme digestion resulted in the loss of about 50% of the pyrrole cross-links. Identification of a series of peptides by mass spectrometry confirmed the presence of derivatized pyrrole structures combined with between 1 and 16 amino acid residues. Almost all of the pyrrole-containing peptides appeared to be derived from N-terminal telopeptide sequences, and the nonhydroxylated (lysine-derived) form predominated over pyrrole cross-links derived from helical hydroxylysine.     

A comparative conformational study of thymidylyl(3'----5')-thymidine, thymidylyl(3'----5')-5'-thio-5'- deoxythymidine and thymidinylacetamido-[3'(O)----5'(C)]-5'-deoxythymidine

A comparative 270 MHz NMR spectroscopic study on the solution structure of the dimer d(TpT) 1, and its two analogues, namely, d(TpST) 2, and NH2d(TcmT) 4 has been reported. Analysis of chemical shifts and coupling constants indicate that: (i) The sugar moieties of the constituent nucleotides are not affected by modification of the internucleotide linkages and adopt preferentially an S-type conformation. (ii) The C4'-C5' bond in the pT part of the modified dimers 2 and 4 shows a large conformational freedom (gamma+ = 32% and 35%, respectively) compared to 1 (gamma+ = 75%). (iii) The population of the trans conformer about C5'-O5' is less important in d(TpST) 2 compared to d(TpT) 1. (iv) The C3'-O3' bond in 2 adopts a trans conformation as in 1. (v) The glycosidic bonds in the modified dimers 2 and 4 showed preferential syn conformation. UV and CD data show that the modified dimers 2 and 4 have poor tendency to stack intramolecularly, they also base pair less efficiently with d(ApA) as compared to d(TpT) 1.     

Design of Lewis acid–base complex: enhancing the stability and first hyperpolarizability of large excess electron compound

In the present paper, a new type of Lewis acid–base complex BX₃???Li@Calix[4]pyrrole (X = H and F) was designed and assembled based on electride molecule Li@calix[4]pyrrole (as a Lewis base) and the electron deficient molecule BX₃ (as a Lewis acid) by employing quantum mechanical calculation. The new Lewis acid–base complex offers an interesting push-excess electron-pull (P-e-P) framework to enhance the stability and nonlinear optical (NLO) response. To measure the nonlinear optical response, static first hyperpolarizabilities (β ₀) are exhibited. Significantly, point-face assembled Lewis acid–base complex BF₃???Li@Calix[4]pyrrole (II) has considerable first hyperpolarizabilities (β ₀) value (1.4?×?10⁶ a.u.), which is about 117 times larger than reported 11,721 a.u. of electride Li@Calix[4]pyrrole. Further investigations show that, in BX₃???Li@Calix[4]pyrrole with P-e-P framework, a strong charge-transfer transition from the ground state to the excited state contributes to the enhancement of first hyperpolarizability. Theory calculation of enthalpies of reaction (Δ_rH⁰) at 298 K demonstrates that it is feasible to synthetize the complexes BX₃???Li@Calix[4]pyrrole. In addition, compared with Li@Calix[4]pyrrole, the vertical ionization potential (VIP) and HOMO–LUMO gap of BX₃???Li@Calix[4]pyrrole have obviously increased, due to the introduction of the Lewis acid molecule BX₃. The novel Lewis acid–base NLO complex possesses not only a large nonlinear optical response but also higher stability.

Romanowsky dyes and romanowsky-Giemsa effect. 1. Azure B, purity and content of dye samples, association (author's transl)

Azure B is the most important Romanowsky dye. In combination with eosin Y it produces the well known Romanowsky-Giemsa staining pattern on the cell. Usually commercial azure B is strongly contaminated. We prepared a sample of azure B-BF4 which was analytically pure and had no coloured impurities. The substance was used to redetermine the molar extinction coefficient epsilon (v)M of monomeric azur B in alcoholic solution. In the maximum of the long wavelength absorption at v = 15.61 kK (lambda = 641 nm) the absorptivity is epsilon (15.61)M = (9.40 +/- 0.15) x 10(4)M-1 cm-1. This extinction coefficient may be used for standardization of dye samples. In aqeuous solution azur B forms dimers and even higher polymers with increasing concentration. The dissociation constant of the dimers, K = 2,2 x 10(-4)M (293 K), and the absorption spectra of pure monomers and dimers in water have been calculated from the concentration dependence of the spectra using an iterative procedure. The molar extinction coefficient of the monomers at 15.47 kK (646 nm) is epsilon (15.47)M = 7.4 x 10(4)M-1 cm-1. The dimers have two long wavelength absorption bands at 14.60 and 16.80 kK (685 and 595 nm) with very different intensities 2 x 10(4) and 13.5 x 10(4)M-1 cm-1. The spectrum of the dimers in aqueous solution is in agreement with theoretical considerations of F?rster (1946) and Levinson et al. (1957). It agrees with an antiparallel orientation of the molecules in the dimers. It may be that dimers bound to a substrate in the cell have another geometry than dimers in solution. In this case the weak long wavelength absorption of the dimers can increase.     

Subunit dimers in sheep spleen apoferritin. The effect on iron storage

Ferritin with high and low iron content, 2000 and 790 iron atoms/molecule, was isolated from the spleens of copper-poisoned and control lambs, respectively. Differences in the iron content in vivo were reflected in the properties of the apoferritin protein shells, since the apoprotein from the low iron ferritin took up iron relatively more slowly (0.52 +/- 0.09) and released it more rapidly (1.68 +/- 0.06) in vitro. Although the two types of apoferritin were indistinguishable in terms of surface charge (pI range 4.98-5.43) and in consisting of both heavy and light subunits, the subunit interactions differed markedly; 40-50% of the subunits of low iron ferritin were in dimers stable to reduction and carboxylmethylation, 4% mercaptoethanol, 8% sodium dodecyl sulfate, and 100 degrees C for 30 min, 70% formic acid, and 30% methanol. Subunit dimers were also observed in liver ferritin from mouse and neonatal pig and were enriched in a low iron fraction of horse spleen ferritin. Based on cyanogen bromide fragmentation and NH2-terminal analysis, the natural and chemically cross-linked subunit dimers had two peptides in common; natural subunit dimers also appeared to have a second region cross-linked, suggesting the possibility of both intra- and intersubunit links in the natural dimers. In sheep spleen ferritin, both heavy and light subunits appeared to participate in subunit dimerization. Natural subunit dimers were enriched in low iron ferritin fractions of all ferritin preparations tested (linear correlation = 0.94) and can explain, at least in part, the previously observed effects of iron core size on the apoferritin shell. Whether the subunit cross-links represent part of the subunit assembly process subsequently cleaved by iron (or copper) or whether the cross-links form after iron core formation in vivo has yet to determined. In either case, it is clear that such post-translational variations can affect iron uptake and release and emphasize the importance of the protein shell in determining the iron storage properties of ferritin.     

Mechanisms and implications of the age-associated decrease in DNA repair capacity.

Skin cancer incidence is clearly linked to UV irradiation and increases exponentially with age. We studied the rate of removal of thymine dimers and (6-4) photoproducts in UV-irradiated human dermal fibroblasts derived from donors of different ages. There was a significant decrease with aging in the repair rates of both thymine dimers and (6-4) photoproducts (P<0.001). In addition, there was an age-associated decrease in the protein levels of ERCC3, PCNA, RPA, XPA, and p53 that participate in nucleotide excision repair. Moreover, the mRNA levels of XPA, ERCC3, and PCNA were significantly reduced with aging, suggesting that these decreases are often regulated at the mRNA level. Furthermore, with age induction of p53 after UV irradiation was significantly reduced. Taken together, our data suggest that the age-associated decrease in the repair of UV-induced DNA damage results at least in part from decreased levels of proteins that participate in the repair process.