Engineering an FMN-based iLOV protein for the detection of arsenic ions.

Over the past few decades, genetically encoded fluorescent proteins have been widely used as efficient probes to explore and investigate the roles of metal ions in biological processes. The discovery of small FMN-based fluorescent proteins, such as iLOV and FbFP, has enabled researchers to exploit these fluorescent reporter proteins for metal-sensing applications. In this study, we report the inherent binding properties of iLOV towards arsenic ions. The fluorescence quenching of iLOV was linearly related to the concentration of arsenic ions, and engineered proteins showed better sensitivity than the wild-type protein. Engineering key residues around the chromophore converted the iLOV protein into a highly sensitive sensor for As3+ ions. iLOVN468S exhibited an improved binding affinity with a dissociation constant of 1.5 µM. Furthermore, the circular dichroism spectra indicated that the fluorescence quenching mechanism might be related to arsenic-protein complex formation. Thus, the reagentless sensing of arsenic can potentially be exploited to determine intracellular or environmental arsenic using a genetically encoded biosensing approach.

DNA Topoisomerase Inhibitory Activity of Constituents from the Fruits of Illicium verum.

Three new compounds, a sesquilignan (1) and two glucosylated phenylpropanoids (2, 3), and seven known compounds (4-10), were isolated from the fruits of Illicium verum HOOK. FIL. (Illiciaceae). The structures of 1-3 were determined based on one and two dimensional (1D- and 2D-) NMR data and electronic circular dichroism (ECD) spectra analyses. Compounds 3, 5, 6, and 8-10 exhibited potent inhibitory activities against topoisomerase II with IC50 values of 54.6, 25.5, 17.9, 12.1, 0.3 and 1.0 µM, respectively, compared to etoposide, the positive control, with an IC50 of 43.8 µM.

DNA Topoisomerase Inhibitory Activity of Constituents from the Flowers of Inula japonica.

Fourteen compounds were isolated from the flowers of Inula japonica THUNB. (Asteraceae), including two new compounds, (1S,2S,4S,5S,8S,10R)-2-acetoxy-4,3-dihydroxy-pseudoguai-7(11)-en-12,8-olide (1) and (1S,2S,4S,5S,8S,10R)-2,4,13-trihydroxy-pseudoguai-7(11)-en-12,8-olide (2), and twelve known compounds, budlein B (3), 6ß-hydroxytomentosin (4), 6-deacetoxybritanin (5), 4-epipulchellin (6), britanin (7), tomentosin (8), (+)-dihydroquercetin (9), (-)-syringaresinol (10), quercetagetin 3,4'-dimethyl ether (11), luteolin (12), britanin G (13) and inuchinenolide C (14). Structures of 1 and 2 were determined based on one and two dimensional (1D)- and (2D)-NMR data and Mosher's esterification method. Compounds 9 and 12 showed inhibitory activities toward DNA topoisomerase I with IC50 values of 55.7 and 37.0 µM, respectively, compared to camptothecin (CPT) with an IC50 of 24.5 µM. Compounds 7-9 and 11-14 exhibited more potent inhibitory activity against topoisomerases II with IC50 values of 6.9, 3.8, 3.0, 6.9, 10.0, 14.7 and 13.8 µM, respectively, than that of etoposide (VP-16) with an IC50 of 26.9 µM. Compounds 4-7 and 10-14 exhibited weak cytotoxicities to the selected cancer cell lines.

Synthesis of novel and diverse mollugin analogues and their antibacterial and antioxidant activities.

Novel and diverse mollugin analogues (1-12) were synthesized using PhB(OH)2/AcOH-mediated electrocyclization reaction as a key step. The newly synthesized compounds were screened for antioxidant and antibacterial activities. Compounds 1, 2, 5, 6, 8, and 10-12 showed high antioxidant activities in DPPH inhibition (IC50=0.52-1.11 µM) compared with BHT (IC50=9.67 µM). Compounds 3 exhibited potent antibacterial activity against Staphylococcus aureus (KCTC-1916) bacterial strain at 100 µg/mL. Structures of newly synthesized compounds were confirmed by IR, (1)H NMR, (13)C NMR data and high-resolution mass spectrometry.

Constituents with DNA topoisomerases I and II inhibitory activity and cytotoxicity from the roots of Rubia cordifolia.

Activity-directed isolation of the ethyl acetate fraction from the roots of Rubia cordifolia resulted in the identification of a new anthraquinone, 1,3,6-trihydroxy-2-hydroxymethyl-9,10-anthraquinone-3- O- α- L-rhamnopyranosyl-(1 → 2)- ß-D-(6'-O-acetyl)-glucopyranoside (1), two new dihydronaphtoquinones, 1,4-dihydroxy-2-carbomethoxy-3-prenylnaphthalene-1-O- ß-D-glucopyranoside (2) and mollugin-1-O- ß- D-glucopyranoside (3), and a new monoterpenoid, 3 R,3a S,4 R,6a R-3,4,6-tris(hydroxymethyl)-3,3a,4,6a-tetrahydro-2 H-cyclopenta[ B]furan-2-one (4), together with nine known compounds (5-13). The structures of these compounds were elucidated on the basis of spectroscopic evidence. In addition, their DNA topoisomerases I and II inhibitory activity and cytotoxicity were measured.

2,6-Dithienyl-4-furyl pyridines: Synthesis, topoisomerase I and II inhibition, cytotoxicity, structure-activity relationship, and docking study.

For the development of novel antitumor agents, 2,6-dithienyl-4-furyl pyridine derivatives were prepared and evaluated for their topoisomerase I and II inhibitory activity as well as cytotoxicity against several human cancer cell lines. Among the 21 prepared compounds, compound 24 exhibited strong topoisomerase I inhibitory activity. In addition, a docking study with topoisomerase I and compound 24 was performed.

Inhibition of DNA topoisomerases I and II and cytotoxicity by lignans from Saururus chinensis.

Thirteen lignans, erythro-austrobailignan-6 (1), meso-dihydroguaiaretic acid (2), sauchinone (3), 1'-epi-sauchinone (4), saucerneol D (5), manassantin B (6), manassantin A (7), nectandrin B (8), machilin D (9), saucerneol F (10), saucerneol G (11), saucerneol H (12) and saucerneol I (13), were isolated from the ethyl acetate extract of the roots of Saururus chinensis. Among these compounds, 5 showed potent inhibitory activities against DNA topoisomerase I and II, and 5, 6, 7 and 10 showed mild cytotoxicities against HT-29 (IC(50) values; 13, 12, 11, and 10 microM, respectively) and HepG2 cell lines (IC(50) values; 16, 11, 12, and 11 microM, respectively).

Lignans from the roots of Saururus chinensis.

Four new lignans, saucerneol F (1), saucerneol G (2), saucerneol H (3), and saucerneol I (4), were isolated from the EtOAc extract of the roots of Saururus chinensis, together with one known compound, saucerneol D (5). The structures of compounds 1-4 were elucidated by spectroscopic analysis. These compounds showed cytotoxic activities against HT-29, MCF-7, and HepG-2 cell lines.

Synthesis of 2,6-diaryl-substituted pyridines and their antitumor activities.

For the development of novel antitumor agents, we designed and synthesized 2,6-diaryl-substituted pyridine derivatives bearing three aryl groups, which are the bioisosteres of terpyridine, and evaluated their biological activities. Most of the 18 prepared compounds showed moderate cytotoxicity against several human cancer cell lines. From the structure-activity relationships we may conclude that the number of aryl groups employed would be critical for their biological activities.

Topoisomerase I and II inhibitory constituents from the bark of Tilia amurensis.

Two coumarins (1 and 6), one flavan-3-ol (2), one fatty acid (3), and two lignan glycosides (4 and 5) were isolated from the EtOAc and CH(2)Cl(2) extract of the bark of Tilia amurensis. Their chemical structures were identified by comparing their physicochemical and spectral data with those of published in literatures. Compounds 4, 5, and 6 were isolated from Tilia genus for the first time. Compounds 2 and 3 showed potent inhibitory activity against both DNA topoisomerase I (IC(50) values; 49 microM and 4 microM, respectively, with 18 microM of positive control compound, comptothecin) and DNA topoisomerase II (IC(50) values; 13 microM and 3 microM, respectively, with 50 microM of positive control compound, etoposide). However, all compounds did not showed cytotoxicity against the human colon adenocarcinoma cell line (HT-29), the human breast adenocarcinoma cell line (MCF-7), and human liver hepatoblastoma cell line (HepG-2).

Cytotoxic and DNA topoisomerases I and II inhibitory constituents from the roots of Aralia cordata.

Bioactivity-guided fractionation, based on the DNA topoisomerase inhibitory activity, lead to the isolation of five compounds (1-5) from the methylene chloride extract of the roots of Aralia cordata Thunb. (Araliaceae). These compounds were identified as ent-pimara-8(14), 15-dien-19-oic acid (1), ent-pimara-8(14), 15-dien-18-oic acid (2), 16alpha-hydrogen-17-isovaleryloxy-ent-kauran-19-oic acid (3), 16alpha-hydroxy-17-isovaleryloxy-ent-kauran-19-oic acid (4) and dehydrofalcarindiol-8-acetate (5) from their spectral data. Compound 3 was isolated for the first time from this plant, and also showed the strongest inhibition of both DNA topoisomerase I and II activities, with 53 and 96% inhibitions, respectively, at a concentration of 20 microM. However, all the compounds exhibited either weak or no cytotoxicities against the human colon carcinoma cell line (HT-29), the human breast carcinoma cell line (MCF-7) and human hepato blastoma cell line (HepG-2).

Cytotoxic constituents isolated from the fruit bodies of Hypsizigus marmoreus.

The bioactivity-guided fractionation of chloroform extracts of the fruit bodies of Hypsizigus marmoreus led to our isolation of (22E,24R)-ergosta-7,22-diene-3beta,5alpha,6beta-triol (1), ergosterol-3-O-beta-D-glucopyranoside (2), 5alpha,8alpha-epidioxyergosta-6,22-dien-3beta-ol (3), hypsiziprenol A9 (4), hypsiziprenol AA8 (5), hypsiziprenol AA9 (6) and hypsiziprenol BA10 (7). Among these seven isolates, compound 2 was identified for the first time from this plant. All compounds (1-7) exhibited moderate cytotoxicity towards cultured human colon carcinoma (HT-29), human breast carcinoma (MCF-7) and human hepatoblastoma (HepG-2) cell lines.

Formation of Cu(II)-brazilin complex in the presence of DNA and its activities as chemical nuclease.

Brazilin, a traditional medicine for the treatment of pain and inflammation, forms a complex with Cu(II) in the presence as well as the absence of DNA. The Cu(II)-brazilin complex exhibited the strand cleavage activity for the pBR322 supercoiled DNA, converting supercoiled form to nicked form. The presence of various scavengers for the oxygen species suppresses or reduces the cleavage activity of the complex, indicating that the DNA cleavage is oxidative. The binding mode of the Cu(II)-brazilin complex was studied by absorption and CD spectroscopy. While a large metal-to-ligand charge transfer (MLCT) band was apparent when Cu(II) and brazilin was mixed in the presence and absence of DNA, the CD did not show any signal in the same region in the presence of DNA, suggesting a weak interaction between the Cu(II)-brazilin complex and DNA bases.

The role of DNA polymerase iota in UV mutational spectra.

UVB (280-320 nm) and UVC (200-280 nm) irradiation generate predominantly cyclobutane pyrimidine dimers (CPDs) and (6-4) photoproducts in DNA. CPDs are thought to be responsible for most of the UV-induced mutations. Thymine-thymine CPDs, and probably also CPDs containing cytosine, are replicated in vivo in a largely accurate manner by a DNA polymerase eta (Pol eta) dependent process. Pol eta is a DNA damage-tolerant and error-prone DNA polymerase encoded by the POLH (XPV) gene in humans. Another member of the Y family of error-prone DNA polymerases is POLI encoding DNA polymerase iota (Pol iota). In order to clarify the specific role of Pol iota in UV mutagenesis, we have used an siRNA knockdown approach in combination with a supF shuttle vector which replicates in mammalian cells, similar as we have previously done for Pol eta. Synthetic RNA duplexes were used to efficiently inhibit Pol iota expression in 293 T cells. The supF shuttle vector was irradiated with 254 nm UVC and replicated in 293 T cells in presence of anti-Pol iota siRNA. Surprisingly, there was a consistent reduction of recovered plasmid from cells with Pol iota knockdown and this was independent of UV irradiation of the plasmid. The supF mutant frequency was unchanged in the siRNA knockdown cells relative to control cells confirming that Pol iota does not play an important role in UV mutagenesis. UV-induced supF mutants were sequenced from siRNA-treated cells and controls. Neither the type of mutations nor their distribution along the supF gene were significantly different between controls and siRNA knockdown cells and were predominantly C to T and CC to TT transitions at dipyrimidine sites. These results show that Pol iota has no significant role in UV lesion bypass and mutagenesis in vivo and provides some initial data suggesting that this polymerase may be involved in replication of extrachromosomal DNA.

Synthesis, cytotoxicity and structure-activity relationship study of terpyridines.

For the development of novel antitumor agents, we designed and synthesized terpyridines, and their biological activities were evaluated. Although most of the newly prepared terpyridines showed strong cytotoxicity against several human cancer cell lines, [2,2';6',2"]-terpyridine displayed the most significant cytotoxicity.

A new stilbene glucoside from the roots of Polygonum multiflorum Thunb.

One new stilbene glucoside (6), along with five known compounds (1-5), were isolated from the roots of Polygonum multiflorum Thumb., and their chemical structures established based on physicochemical and spectroscopic data. Of the compounds, compound 3 showed DNA topoisomerase I and II inhibitory activities.

Cytotoxicity and DNA topoisomerase inhibitory activity of constituents isolated from the fruits of Evodia officinalis.

Four alkaloids (1-4), three quinolone alkaloids (5-7), and three flavanoid glucosides (8-10) were isolated from the fruits of Evodia officinalis Dode, and their structures were determined from chemical and spectral data. Compounds, 3, 8, 9 and 10 were isolated from this plant for the first time. Of these compounds, 1-3 and 5-7 exhibited moderate cytotoxicities against cultured human colon carcinoma (HT-29), human breast carcinoma (MCF-7), and human hepatoblastoma (HepG-2). Compound 8 showed strong inhibitory effects on DNA topoisomerases I and II (70 and 96% inhibition at a concentration of 20 microM, respectively).

FMN-Based Fluorescent Proteins as Heavy Metal Sensors Against Mercury Ions.

Bacterial light-oxygen-voltage-sensing photoreceptor-derived flavin mononucleotide (FMN)- based fluorescent proteins act as a promising distinct class of fluorescent proteins utilized for various biomedical and biotechnological applications. The key property of its independency towards oxygen for its chromophore maturation has greatly helped this protein to outperform the other fluorescent proteins such as GFP and DsRed for anaerobic applications. Here, we describe the feasibility of FMN-containing fluorescent protein FbFP as a metal-sensing probe by measuring the fluorescence emission changes of a protein with respect to the concentration of metal ions. In the present study, we demonstrated the mercury-sensing ability of FbFP protein and the possible amino acids responsible for metal binding. A ratiometric approach was employed here in order to exploit the fluorescence changes observed at two different emission maxima with respect to Hg(2+) at micromolar concentration. The engineered variant FbFPC56I showed high sensitivity towards Hg(2+) and followed a good linear relationship from 0.1 to 3 µM of Hg(2+). Thus, further engineering with a rational approach would enable the FbFP to be developed as a novel and highly selective and sensitive biosensor for other toxic heavy metal ions as well.

DNA sequence analysis of 1-nitropyrene-4,5-oxide and 1-nitropyrene-9,10-oxide induced mutations in the hprt gene of Chinese hamster ovary cells.

Nitropyrene, the predominant nitropolycyclic hydrocarbon found in diesel exhaust, is a mutagenic and tumorigenic environmental pollutant that requires metabolic activation via nitroreduction and ring oxidation. In order to determine the role of ring oxidation in the mutagenicity of 1-nitropyrene, its oxidative metabolites, 1-nitropyrene 4,5-oxide and 1-nitropyrene 9,10-oxide, were synthesized and their mutation spectra were determined in the coding region of hprt gene of CHO cells by a PCR amplification of reverse-transcribed hprt mRNA, followed by a DNA sequence analysis. A comparison of the two metabolites for mutation frequencies showed that 1-nitropyrene 9,10-oxide was 2-times higher than 1-nitropyrene 4,5-oxide. The mutation spectrum for 1-nitropyrene 4,5-oxide was base substitutions (33/49), one base deletions (11/49) and exon deletions (5/49). In the case of 1-nitropyrene 9,10-oxide, base substitutions (27/50), one base deletions (15/50), and exon deletions (8/50) were observed. Base substitutions were distributed randomly throughout the hprt gene. The majority of the base substitutions in mutant from 1-nitropyrene 4,5-oxide treated cells were A-->G transition (15/33) and G-->A transition (8/33). The predominant base substitution, A-->G transition (11/27) and G-->A transition (8/27), were also observed in mutant from 1-nitropyrene 9,10-oxide treated cells. The mutation at the site of adenine and guanine was consistent with the previous results, where the sites of DNA adduct formed by these compounds were predominant at the sites of purines. A comparison of the mutational patterns between 1-nitropyrene 4,5-oxide and 1-nitropyrene 9,10-oxide showed that there were no significant differences in the overall mutational spectrum. These results indicate that each oxidative metabolite exhibits an equal contribution to the mutagenicity of 1-nitropyrene, and ring oxidation of 1-nitropyrene is an important metabolic pathway to the formation of significant lethal DNA lesions.

Incorporating unnatural amino acids to engineer biocatalysts for industrial bioprocess applications.

The bioprocess engineering with biocatalysts broadly spans its development and actual application of enzymes in an industrial context. Recently, both the use of bioprocess engineering and the development and employment of enzyme engineering techniques have been increasing rapidly. Importantly, engineering techniques that incorporate unnatural amino acids (UAAs) in vivo has begun to produce enzymes with greater stability and altered catalytic properties. Despite the growth of this technique, its potential value in bioprocess applications remains to be fully exploited. In this review, we explore the methodologies involved in UAA incorporation as well as ways to synthesize these UAAs. In addition, we summarize recent efforts to increase the yield of UAA engineered proteins in Escherichia coli and also the application of this tool in enzyme engineering. Furthermore, this protein engineering tool based on the incorporation of UAA can be used to develop immobilized enzymes that are ideal for bioprocess applications. Considering the potential of this tool and by exploiting these engineered enzymes, we expect the field of bioprocess engineering to open up new opportunities for biocatalysis in the near future.