Synthesis of nucleobase-caged peptide nucleic acids having improved photochemical properties.

A nucleobase-caged peptide nucleic acid (PNA) having a (6-bromo-7-methoxycoumarin)-4-ylmethoxycarbonyl (Bmcmoc) caging group was newly synthesized. The Bmcmoc-caged PNAs were photolyzed to produce parent PNAs with a high photochemical efficiency. Introduction of a single Bmcmoc group was sufficient to suppress polymerase chain reaction (PCR) clamping activity and triplex invasion complex formation. Photo-mediated restoration of the PCR clamping activity was also demonstrated.

Fluorophore labeling enables imaging and evaluation of specific CXCR4-ligand interaction at the cell membrane for fluorescence-based screening.

Development of CXCR4-specific ligands is an important issue in chemotherapy of HIV infection, cancer metastasis, and rheumatoid arthritis, and numerous potential ligands have been developed to date. However, it is difficult to assess their binding mode and specificity because of uncertainties in the structure of the CXCR4-ligand complexes. To address this problem, we have synthesized fluorophore labeled Ac-TZ14011, which is derived from T140, a powerful CXCR4 antagonist. Binding of Ac-TZ14011 to CXCR4 on the cell membrane was observed by fluorescence microscope, and analysis of the binding data produced IC 50 values of several ligands comparable to those obtained in RI-based assays. This fluorescence-based assay is applicable to explore new pharmacophores of CXCR4-specific ligands with high-throughput screening and also to screening of the other GPCR binding ligands.

Structure-activity relationship study of CXCR4 antagonists bearing the cyclic pentapeptide scaffold: identification of the new pharmacophore.

A highly potent CXCR4 antagonist 2 [cyclo (-D-Tyr1-Arg2-Arg3-Nal4-Gly5-)] has previously been identified by screening cyclic pentapeptide libraries that were designed based on pharmacophore residues of a 14-residue peptidic CXCR4 antagonist 1. In the present study, D-Tyr and Arg in peptide 2 were replaced by a bicyclic aromatic amino acid and a cationic amino acid, respectively, and their binding activity for CXCR4 was evaluated for identification of the novel pharmacophore.

Role of humic acid fraction with higher aromaticity in enhancing the activity of a biomimetic catalyst, tetra(p-sulfonatophenyl)porphineiron(III).

To elucidate the structural features of humic acids (HAs) that potentially contribute to enhancing the activity of a tetra(p-sulfonatophenyl)porphineiron(III) (Fe(III)-TPPS) catalyst, the effects of the chemical properties of molecular weight fractionated HAs on the catalytic activity of Fe(III)-TPPS were investigated. Three fractions were obtained as the following order of molecular size: F3 < F2 < F1. The deactivation of Fe(III)-TPPS, which can be attributed to the self-degradation of Fe(III)-TPPS, was retarded in the presence of HAs, and the pseudo-first-order rate constant in the presence of F3 was the smallest of the three fractions. In addition, the highest catalytic activity, determined as the percent degradation of an organic substrate, was observed in the presence of F3. The enhanced catalytic activity of Fe(III)-TPPS was due to the formation of supramolecular complexes with HAs, and the formation constant for F3 was the largest. Thus, the F3 fraction was the most effective fraction. Solid-state CPMS 13C NMR spectra indicated that the aromaticity of F3 was the highest of all of the fractions. Thus, it can be concluded that aromatic moieties in HAs play an important role in the formation of supramolecular complexes with Fe(III)-TPPS, leading to an enhancement in catalytic activity.

Water solubility enhancement effects of some polychlorinated organic pollutants by dissolved organic carbon from a soil with a higher organic carbon content.

To elucidate the role of a soil humic acid (HA) in the transport of polychlorinated organic pollutants (PCOPs), such as polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans and coplanar-polychlorinated biphenyls, their partition coefficients (Kdoc) into an HA were compared with their adsorption coefficients (KOC) for a soil with a higher organic carbon (OC) content. The soil sample (ando soil) used in the present study was collected in the same location as the HA. The log Kdoc values were positively correlated with logarithm of octanol-water partition coefficients (log KOW) of the PCOPs, indicating that the partitioning of PCOPs into the HA was mainly due to hydrophobic interactions. However, the correlation between log Kdoc and log KOC was negative. This can be attributed to the enhanced water solubility of the PCOPs as the result of the dissolved organic matter from the soil. That is, when the more hydrophobic PCOPs with higher log KOW values are partitioned into the HA, then the larger quantities of PCOPs that are partitioned into the HA are able to dissolve in the aqueous phase. These results suggest that, in a soil with a higher OC content, the HA can serve as more effective carrier of PCOPs from the soil to an aquatic environment.