Comparative Circular Dichroism Research Articles

New Metabolites from the South China Sea Sponge Diacarnus megaspinorhabdosa.

Chemical investigation on CH2Cl2 extract of the marine sponge Diacarnus megaspinorhabdosa resulted in the isolation of two new farnesylacetone derivatives 1-2, a new γ-lactone 3, a known dinorditerpenone 4 and four known norsesterterpene peroxides 5-8. Their structures were elucidated by using one and two dimensional (1D and 2D)-NMR, high resolution-electrospray ionization (HR-ESI)-MS, and comparison with the literature. Compounds 1 and 2 were cis/trans-olefinic isomers and determined through nuclear Overhauser effect spectroscopy (NOESY) experiment. The absolute configuration of 3 was established by comparison of circular dichroism (CD) data with known lactones. The cytotoxic activities of the compounds were evaluated against five cancer cell lines, and compound 3 showed moderate cytotoxicity activities against cancer cell lines HeLa, H446, NCI-H460, SGC-7901 and MCF-7, with IC50 values in the range of 18.5 to 47.1 µM.

ChemInform Abstract: Saliniquinones A—F, New Members of the Highly Cytotoxic Anthraquinone‐γ‐pyrones from the Marine Actinomycete Salinispora arenicola.

Six new anthraquinone-γ-pyrones, saliniquinones A-F (1-6), which are related to metabolites of the pluramycin/altromycin class, were isolated from a fermentation broth of the marine actinomycete Salinispora arenicola (strain CNS-325). Their structures were determined by analysis of one- and two-dimensional NMR spectroscopic and high-resolution mass spectrometric data. The relative and absolute configurations of compounds 1-6 were determined by analysis of NOESY NMR spectroscopic data and by comparison of circular dichroism and optical rotation data with model compounds found in the literature. Saliniquinone A (1) exhibited potent inhibition of the human colon adenocarcinoma cell line (HCT-116) with an IC50 of 9.9 × 10-9 M. In the context of the biosynthetic diversity of S. arenicola, compounds 1-6 represent secondary metabolites that appear to be strain specific and thus occur outside of the core group of compounds commonly observed from this species.

Gamma Ray Irradiation of the Vasoactive Peptide Bradykinin Reveals a Residue- and Position-Dependent Structural Modification

In this work the effect of radical species generated by gamma ray irradiation of aqueous solution upon structure of vasoactive peptide bradykinin (BK, RPPGFSPFR) was investigated. Increasing doses of 1–15 kGy Co60 gamma radiation were applied to BK solutions and a progressive degradation of its structure in a non-linear mode was observed. Two main peptide derivatives generated by these treatments were isolated and characterized through a combined amino acid analysis and daughter ion scanning mass spectrometry approach. Notably, it was observed that only the Phe residue located at position 8 and not 5 of BK was oxidized by reactive hydroxyl radical species given rise to Tyr8-BK and m-Tyr8-BK analogues. Comparative circular dichroism (CD) experiments of these peptides revealed that BK presents greater conformational similarity to Tyr8-BK than to m-Tyr8-BK. These results are in agreement with the biological potencies of these compounds measured in rat uterus and guinea pig ileum muscle contractile experiments. In summary, gamma irradiation of BK solutions revealed a residue- and surprisingly, position-structural modification effect of reactive radicals even in small peptides. Also of value for peptide chemistry field, the approach of applying controlled strong electromagnetic radiation in solution seems to be an alternative and unique strategy for generating, in some cases, peptides derivatives with uncommon structures and valuable for their further therapeutic potential evaluations.

Saliniquinones A - F, New Members of the Highly Cytotoxic Anthraquinone-γ-Pyrones from the Marine Actinomycete Salinispora arenicola

Six new anthraquinone-γ-pyrones, saliniquinones A-F (1-6), which are related to metabolites of the pluramycin/altromycin class, were isolated from a fermentation broth of the marine actinomycete Salinispora arenicola (strain CNS-325). Their structures were determined by analysis of one- and two-dimensional NMR spectroscopic and high-resolution mass spectrometric data. The relative and absolute configurations of compounds 1-6 were determined by analysis of NOESY NMR spectroscopic data and by comparison of circular dichroism and optical rotation data with model compounds found in the literature. Saliniquinone A (1) exhibited potent inhibition of the human colon adenocarcinoma cell line (HCT-116) with an IC50 of 9.9 × 10-9 M. In the context of the biosynthetic diversity of S. arenicola, compounds 1-6 represent secondary metabolites that appear to be strain specific and thus occur outside of the core group of compounds commonly observed from this species.

Formation of Pseudosymmetrical G-Quadruplex and i-Motif Structures in the Proximal Promoter Region of the RET Oncogene

A polypurine (guanine)/polypyrimidine (cytosine)-rich sequence within the proximal promoter region of the human RET oncogene has been shown to be essential for RET basal transcription. Specifically, the G-rich strand within this region consists of five consecutive runs of guanines, which is consistent with the general motif capable of forming intramolecular G-quadruplexes. Here we demonstrate that, in the presence of 100 mM K+, this G-rich strand has the ability to adopt two intramolecular G-quadruplex structures in vitro. Moreover, comparative circular dichroism (CD) and DMS footprinting studies have revealed that the 3'-G-quadruplex structure is a parallel-type intramolecular structure containing three G-tetrads. The G-quadruplex-interactive agents TMPyP4 and telomestatin further stabilize this G-quadruplex structure. In addition, we demonstrate that the complementary C-rich strand forms an i-motif structure in vitro, as shown by CD spectroscopy and chemical footprinting. This 19-mer duplex sequence is predicted to form stable intramolecular G-quadruplex and i-motif species having minimum symmetrical loop sizes of 1:3:1 and 2:3:2, respectively. Together, our results indicate that stable G-quadruplex and i-motif structures can form within the proximal promoter region of the human RET oncogene, suggesting that these secondary structures play an important role in transcriptional regulation of this gene.

Regio‐ and Diastereoselective Synthesis of Bis‐ and Tetrakisadducts of C70 by Directed Remote Functionalization Using Tröger Base Tethers

Double Bingel cyclopropanation of C70 with bismalonates featuring Tröger base derivatives as chiral spacers afforded bisadducts with almost perfect regio- and stereoselectivity. The excellent directing property of these rigidly folded spacers in the remote functionalization of the higher fullerene was further highlighted by the selective formation of a product with a novel bisaddition pattern involving the C(7)-C(22) and C(33)-C(34) bonds of C70. Enantiomerically pure bisadducts of C70 were prepared by highly diastereoselective transformations of bismalonates incorporating optically pure Tröger base tethers. The absolute configuration of these bisadducts was established by comparison of circular dichroism (CD) spectra with data reported in the literature. For the first time, optically active tetrakisadducts of a fullerene were prepared by two sequential chiral-spacer-controlled remote functionalizations.

Conformational properties of 2',5' linked Rp- and Sp-phosphorothioate oligoadenylates studied by circular dichroism and NMR.

2',5'-Linked oligoadenylates (2-5A) are involved in the antiviral action of interferon. The 2-5A binds and activates 2-5A dependent RNase (RNase L), which degrades viral mRNA, resulting in the inhibition of protein synthesis. 2',5'-Linked phosphorothioate oligoadenylates with an Rp configuration bind to and activate the RNase L. On the other hand, 2',5' phosphorothioate oligoadenylate with an Sp configuration weakly binds to the RNase L and is devoid of the RNase L activation ability. Comparative circular dichroism (CD) and NMR studies are carried out to characterize the difference in properties between the two configurations of the 2',5' phosphorothioate oligoadenylates. 2',5' Rp-Phosphorothioate oligoadenylates showed CD spectra similar to those of the corresponding native 2',5' oligoadenylates, while the 2',5' Sp-phosphorothioate oligoadenylates exhibited a weaker CD band compared to the former two, indicating the weaker base-stacking interaction of the 2',5' Sp-phosphorothioate oligoadenylates. The temperature-dependent change in the CD revealed that 2',5' phosphorothioate oligoadenylates showed larger DeltaH(0) and DeltaS(0) values for the thermal transition of the conformation than the corresponding native 2',5' oligoadenylates. The NMR spectral assignment was accomplished by several NMR measuring techniques. The 2'-H of the ribose ring linked to the 2',5' Sp-phosphorothioate showed a higher field chemical shift of the proton NMR than that linked to the corresponding 2',5' Rp-phosphorothioate. 2',5' Rp- and Sp-phosphorothioate oligoadenylates possess a sugar conformation similar to that of the corresponding native 2',5' oligoadenylates.

A new alkaloid from the purple Indian Ocean tunicate Eudistoma bituminis

A new alkaloid, segoline C 1 possessing the benzo 1,6-diazaphenanthroline ring system has been isolated from the Indian Ocean tunicate Eudistoma bituminis with the known segoline A 2 isolated from the Red Sea tunicate Eudistoma sp. The structure of all compounds was elucidated on the basis of spectroscopic data. The relative configuration of the chiral compound 1 is proposed on the basis of comparative circular dichroism (CD) measurements of segolines A 2 and B 3 .

Conformational Preferences of RNase A C-Peptide Derivatives Containing a Highly Constrained Analogue of Phenylalanine

Both enantiomers of a highly constrained derivative of phenylalanine, FiFi, were prepared in optically pure form. Studies were performed to elucidate the effects of substituting this amino acid for phenylalanine in RN-24, a derivative of the RNase A C-peptide. Thus RN-24, and the analogues 9 and 10, in which Phe-8 was replaced by each of the enantiomers of FiFi, were prepared. Comparative circular dichroism (CD) experiments indicated relative tendencies to adopt helical structures, and variable-temperature CD studies showed the relative ease with which these conformations were lost at elevated temperatures. These observations were rationalized via computer-assisted molecular modeling, which showed that the phenyl groups of (R,R)-FiFi in the peptidomimetic 9 can be accommodated via distortion of the helical conformations and that such distorted conformations persist as the temperature is increased. Conversely, intolerable contacts occur in an analogous conformation of the (S,S)-FiFi peptidomimetic 10 and t...

Macrocyclic zinc(II) complexes for selective recognition of nucleobases in single- and double-stranded polynucleotides

As an extension of our earlier discoveries that ZnII-cyclen complex (1) (cyclen=1,4,7,10-tetraazacyclododecane) and ZnII-acridine-pendant cyclen complex ZnII-N-(9-acridin)ylmethyl-cyclen (3) are the first compounds to selectively recognize thymidine and uridine nucleosides in aqueous solution at physiological pH, the interaction of these and a relevant complex, bis(ZnII-cyclen) (7), has been investigated with a series of polynucleotides, single-stranded poly(U) and poly(G), and double-stranded poly(A)·poly(U), poly(dA)·poly(dT) and poly(dG)·poly(dC). These ZnII-cyclen complexes interact with the imide-containing nucleobases in the single-stranded poly(U), unperturbed by the presence of the anionic phosphodiester backbone. The affinity constant of 1 for each N(3)-deprotonated uracil base in poly(U) is determined to be log K= 5.1 by a kinetic measurement, which is almost the same as log K=5.2 for the interaction of 1 with uridine. Thus, they disrupt the A-U (or A-T) hydrogen bonds to unzip the duplex of poly(A)·poly(U) or poly(dA)·poly(dT), as demonstrated by lowering of the melting temperatures (Tm) of poly(A)·poly(U) and poly(dA)·poly(dT) in 5 mM Tris-HCl buffer (pH 7.6, 10 mM NaCl) with increase in their concentrations. The order of the denaturing efficiency is well correlated with that of the 1 : 1 affinity constants for each complex with uracil or thymine;7>3>1. The comparison of circular dichroism (CD) spectra for poly(A)·poly(U), poly(A), and poly(U) in the presence of 3 has revealed a structural change from poly(A)·poly(U) to two single strands, poly(A) and poly(U), caused by 3 binding exclusively to uracils in poly(U). On the other hand, the acridine-pendant cyclen complex 3, which earlier was found to associate with guanine by the ZnII coordinating with guanine N(7), in addition to the π-π stacking, interacts with guanine in the double helix of poly(dG)·poly(dC) from outside and stabilized the double-stranded structure, as indicated by higher Tm.

Macrocyclic metal complexes for selective recognition of nucleic acid bases and manipulation of gene expression

Abstract

Thermal unfolding of bovine alpha-lactalbumin. Comparison of circular dichroism with hydrophobicity measurements.

The thermal unfolding of apo- and Ca(2+)-loaded bovine alpha-lactalbumin (BLA) determined by circular dichroism measurements at 220 and 270 nm is related to the exposure of its hydrophobic surface measured by the interaction with 1,1'-bi(4-anilino)naphthalene-5,5'-disulfonate. The results indicate that several (about 5) probe molecules are able to bind with low affinity to the compact surface of the native protein. By thermal destabilization to the molten globule state, access is given to two domains with strong hydrophobic character. On further heating the hydrophobic domains degenerate; however, the temperature of destabilization is different for the two domains. A comparable evolution of the hydrophobic behavior is observed for apo- and Ca(2+)-BLA, but the destabilization steps of Ca(2+)-BLA occur at higher temperatures than those of apo-BLA. Also, it has not been reported earlier that, at a moderate Ca2+ concentration (2 mM), Ca2+ remains associated with BLA after the thermally induced destabilization of its native tertiary structure. At 70 degrees C, a partially unfolded state of Ca(2+)-loaded BLA is obtained.

Synthesis, separation and absolute configuration assignment to enantiomers of 1,3-benzodithiole 1-oxide and 2-alkyl-1,3-benzodithiole 1-oxides

1,3-Benzodithiole 1-oxide, 5, has been resolved into enantiomers using chiral stationary phase high performance liquid chromatography. Alkylation of an excess (25%) of the late eluting (+)-(1R) enantiomer of the sulfoxide 5 under basic conditions yielded both cis and trans isomers of 2-methyl (6cis-1R,2S′,6trans-1R,2R), 2-ethyl (7cis-1R,2S′, 7trans-1R,2R) and 2-isopropyl (8cis-1R,2S′, 8trans-1R,2R)-benzodithiole 1-oxide (25% e.e.) and allowed a stereochemical correlation of absolute configuration between the sulfoxides 5–8.Treatment of racemic 1,3-benzodithiole 1-oxide (51S/51R) with potassium bis(trimethylsilyl)amide and (S)-(+)-1-iodo-2-methylbutane yielded four diastereoisomers of 2-(2′-methylbutyl)-1,3-benzodithiole 1-oxide (9cis-1R,2S,2′S′, 9cis-1S,2R,2′S′, 9trans-1S,2S,2′S, 9trans-1R,2R,2′S) which were separated by chiral stationary phase HPLC (CSP-HPLC). The most strongly retained diastereoisomer was analysed by X-ray crystallography and was assigned the (1S:2S:2′S) absolute configuration. Further alkylation of 9trans-1S,2S,2′S under similar conditions yielded 2-(2′S-methylbutyl)-2-(2″S-methylbutyl)-1,3·benzodithiole 1-oxide 10 of (1S,2′S,2″S) configuration exclusively. The same stereoisomer of the sulfoxide 10 was also obtained by dialkylation of the early eluting (–)-enantiomer of 1,3-benzodithiole 1-oxide (51S) using (+)-1-iodo-2-methylbutane, thus enabling the unequivocal establishment of the absolute configurations of the enantiomers of 1,3-benzodithiole 1-oxides listed in Table 1. A comparison of circular dichroism (CD) spectra for sulfoxides 5–9 indicates that this method may also be used to correlate absolute configurations of 2-alkyl substituted 1,3-benzodithiole 1-oxides.

The DNA binding site of the Xenopus transcription factor IIIA has a non-B-form structure.

On the basis of nuclease digestion studies we proposed that the DNA binding site of transcription factor IIIA (TFIIIA) may have an overall structure with A-type rather than B-type characteristics. This proposal was substantiated by the crystal structure of a part of the TFIIIA binding site. Recently, however, it has been reported that the binding site for TFIIIA is B-form in solution, thus implying that the conformation present in crystals is not the structure in solution. We have carried out a study using comparative circular dichroism (CD) spectroscopy of a number of double stranded deoxyoligonucleotides of different sequence, and known crystal structure. The correlation we have found between CD characteristics and certain structural parameters indicates that the solution and crystal structures of the TFIIIA binding site are closely related. This structure may be classed as an intermediate type, between A-form and B-form DNA.

The 2-nitrophenylsulphenyl chromophoric derivative of the α-amino-group as a circular dichroism probe for the β-structure in oligo-tyrosine peptides

A comparison of circular dichroism (c.d) spectra has revealed that the randomly coiled lower oligomers of the Nps[L-Tyr(Bzl)]nGly-OPEG-M [n= 3–8, Nps = 2-nitrophenylsulphenyl, Bzl = PhCH2, OPEG-M = poly(ethylene glycol monomethyl ether)] peptide series have a positive Cotton effect at 350–400 nm, associated with the 2-nitrophenylsulphenylamino-chromophore, while the β-forming higher oligomers have a negative Cotton effect in that region of their spectra, this suggests the use of the Nps group at the N-terminus as a c.d. probe for β-structure in oligo-Tyr-peptides.

Comparisons of Circular Dichroism in Liquid Solution and in the Crystal State with Reference to Conformations of 3,3'-Bithienyls.

Comparisons of Circular Dichroism in Liquid Solution and in the Crystal State with Reference to Conformations of 3,3'-Bithienyls.

Zuordnung von optisch aktiven Absorptionsbanden in trigonalen Komplexen des dreiwertigen Chroms und Kobalts

AbstractThe comparison of circular dichroism or rotatory dispersion data leads to a classification of trigonal coordination compounds (symmetry D3, C3) of trivalent chromium and cobalt according to the size of the metal‐ligand‐metal ring (five‐ or six‐membered ring, without or with n‐bonding). Within these classes an assignment of the optically active absorption bands is proposed.