Synthesis and photochemical properties of photo-cleavable crosslinkers

Synthesis and antioxidant activities of phenol derivatives from 1,6-bis(dimethoxyphenyl)hexane-1,6-dione

Starting from the compound (3,4-dimethoxyphenyl)(2-(3,4-dimethoxyphenyl)cyclopent-1-en-1-yl)methanone (4), two diols and three tetrol derivatives were synthesised. Morover, from the reactions of 1,3-dimethoxybenzene and 1,4-dimethoxybenzene with adipoyl chloride, fifteen new along with nine known compounds were obtained. For the characterizations of compounds, spectroscopic methods such as NMR including DEPT, COSY, HMQC and HMBC experiments and X-ray diffraction were used. The antioxidant activities of novel synthesized seventeen molecules were investigated by analytical methods like ABTS^•+ and DPPH^• scavenging. Also, reducing power these molecules were investigated by Fe³⁺, Cu²⁺, and [Fe³⁺-(TPTZ)₂]³⁺. Some of the molecules record powerful antioxidant profile when compared to putative standards. The inhibition effects of the phenols compounds against AChE and BChE activities were analysed. Also, these phenols were found as effective inhibitors for AChE, hCA I, hCA II, and BChE with K_is in the range of 122.95 ± 18.41-351.31 ± 69.12 nM for hCA I, 62.35 ± 9.03-363.17 ± 180.1 nM for hCA II, 134.57 ± 3.99-457.43 ± 220.10 nM for AChE, and 27.06 ± 9.12-72.98 ± 9.53 nM for BChE, respectively.

A Two-Photon-Photocleavable Linker for Triggering Light-Induced Strand Breaks in Oligonucleotides

We synthesized a two-photon-sensitive photocleavable linker based on the 7-diethylaminocoumarin structure and introduced it successfully into DNA strands. First, we demonstrated the inducibility of strand scissions upon irradiation at 365 nm. To verify and visualize the two-photon activity, we used a fluorescence assay based on a DNA strand displacement immobilized in a hydrogel. Additionally, we investigated its use in a new class of DNA decoys that are able to catch and release nuclear factor κB (NF-κB) by using light as an external trigger signal. In cell culture we were able to show the regulation of NF-κB-controlled transcription of green fluorescent protein.

Synthesis of 4-[2-(3,4-dimethoxybenzyl)cyclopentyl]-1,2-dimethoxybenzene Derivatives and Evaluations of Their Carbonic Anhydrase Isoenzymes Inhibitory Effects

Rearrangement of 1,6-bis(3,4-dimethoxyphenyl)hexane-1,6-dione (8) gave two isomeric products having cyclopentene moiety. Starting from the major product (3,4-dimethoxyphenyl)[2-(3,4-dimethoxyphenyl)cyclopent-1-en-1-yl]methanone (11), eight new compounds (16-23) were obtained by the reactions such as reduction (by catalytic hydrogenation and NaBH4 ), nitration, 1,4-addition, bromination, and esterification reactions. Carbonic anhydrases (CA, E.C.4.2.1.1) are ubiquitous metalloenzymes present in almost all living organism that catalyze a simple reaction, the conversion of carbon dioxide (CO2 ) and water (H2 O) to bicarbonate ion (HCO3 (-) ) and a proton (H(+) ). CA isoenzymes I and II (hCA I and II) inhibition effects of synthesized eleven new and four known compounds (8-13 and 15-23) were investigated. Inhibition studies of the hCA I and II with 4-[2-(3,4-dimethoxybenzyl)cyclopentyl]-1,2-dimethoxybenzene derivatives revealed that they possess effective inhibitory potency. Cytosolic hCA I and II isoenzymes were potently inhibited by new synthesized 4-[2-(3,4-dimethoxybenzyl)cyclopentyl]-1,2-dimethoxybenzene derivatives with Ki s in the range of 313.16-1537.00 nm against hCA I and in the range of 228.31-1927.31 nm against hCA II, respectively.

Photo-assisted peptide enrichment in protein complex cross-linking analysis of a model homodimeric protein using mass spectrometry

MS analysis of cross-linked peptides can be used to probe protein contact sites in macromolecular complexes. We have developed a photo-cleavable cross-linker that enhances peptide enrichment, improving the signal-to-noise ratio of the cross-linked peptides in mass spectrometry analysis. This cross-linker utilizes nitro-benzyl alcohol group that can be cleaved by UV irradiation and is stable during the multiple washing steps used for peptide enrichment. The enrichment method utilizes a cross-linker that aids in eliminating contamination resulting from protein-based retrieval systems, and thus, facilitates the identification of cross-linked peptides. Homodimeric pilM protein from Pseudomonas aeruginosa 2192 (pilM) was investigated to test the specificity and experimental conditions. As predicted, the known pair of lysine side chains within 14 Å was cross-linked. An unexpected cross-link involving the protein's amino terminus was also detected. This is consistent with the predicted mobility of the amino terminus that may bring the amino groups within 19 Å of one another in solution. These technical improvements allow this method to be used for investigating protein-protein interactions in complex biological samples.

Photochemical tools to study dynamic biological processes

Light-responsive biologically active compounds offer the possibility to study the dynamics of biological processes. Phototriggers and photoswitches have been designed, providing the capability to rapidly cause the initiation of wide range of dynamic biological phenomena. We will discuss, in this article, recent developments in the field of light-triggered chemical tools, specially how two-photon excitation, "caged" fluorophores, and the photoregulation of protein activities in combination with time-resolved x-ray techniques should break new grounds in the understanding of dynamic biological processes.