Dual C-Br Isotope Fractionation Indicates Distinct Reductive Dehalogenation Mechanisms of 1,2-Dibromoethane in Dehalococcoides- and Dehalogenimonas-Containing Cultures.

Brominated organic compounds such as 1,2-dibromoethane (1,2-DBA) are highly toxic groundwater contaminants. Multi-element compound-specific isotope analysis bears the potential to elucidate the biodegradation pathways of 1,2-DBA in the environment, which is crucial information to assess its fate in contaminated sites. This study investigates for the first time dual C-Br isotope fractionation during in vivo biodegradation of 1,2-DBA by two anaerobic enrichment cultures containing organohalide-respiring bacteria (i.e., either Dehalococcoides or Dehalogenimonas). Different εbulkC values (-1.8 ± 0.2 and -19.2 ± 3.5‰, respectively) were obtained, whereas their respective εbulkBr values were lower and similar to each other (-1.22 ± 0.08 and -1.2 ± 0.5‰), leading to distinctly different trends (ΛC-Br = Δδ13C/Δδ81Br ≈ εbulkC/εbulkBr) in a dual C-Br isotope plot (1.4 ± 0.2 and 12 ± 4, respectively). These results suggest the occurrence of different underlying reaction mechanisms during enzymatic 1,2-DBA transformation, that is, concerted dihaloelimination and nucleophilic substitution (SN2-reaction). The strongly pathway-dependent ΛC-Br values illustrate the potential of this approach to elucidate the reaction mechanism of 1,2-DBA in the field and to select appropriate εbulkC values for quantification of biodegradation. The results of this study provide valuable information for future biodegradation studies of 1,2-DBA in contaminated sites.

Enzymatic bypass of an N6-deoxyadenosine DNA-ethylene dibromide-peptide cross-link by translesion DNA polymerases.

Unrepaired DNA-protein cross-links, due to their bulky nature, can stall replication forks and result in genome instability. Large DNA-protein cross-links can be cleaved into DNA-peptide cross-links, but the extent to which these smaller fragments disrupt normal replication is not clear. Ethylene dibromide (1,2-dibromoethane) is a known carcinogen that can cross-link the repair protein O6-alkylguanine-DNA alkyltransferase (AGT) to the N6 position of deoxyadenosine (dA) in DNA, as well as four other positions in DNA. We investigated the effect of a 15-mer peptide from the active site of AGT, cross-linked to the N6 position of dA, on DNA replication by human translesion synthesis DNA polymerases (Pols) η, ⍳, and κ. The peptide-DNA cross-link was bypassed by the three polymerases at different rates. In steady-state kinetics, the specificity constant (kcat/Km) for incorporation of the correct nucleotide opposite to the adduct decreased by 220-fold with Pol κ, tenfold with pol η, and not at all with Pol ⍳. Pol η incorporated all four nucleotides across from the lesion, with the preference dT > dC > dA > dG, while Pol ⍳ and κ only incorporated the correct nucleotide. However, LC-MS/MS analysis of the primer-template extension product revealed error-free bypass of the cross-linked 15-mer peptide by Pol η. We conclude that a bulky 15-mer peptide cross-linked to the N6 position of dA can retard polymerization and cause miscoding but that overall fidelity is not compromised because only correct pairs are extended.

Nucleophilic Thiol Proteins Bind Covalently to Abasic Sites in DNA.

In the course of studies on the enhancement of 1,2-dibromoethane-induced DNA base pair mutations by O6-alkylguanine-DNA alkyltransferase (AGT, MGMT), we discovered the facile reaction of AGT with an abasic site in DNA, leading to covalent cross-linking. The binding of AGT differs from the mechanism reported for the protein HMCES; instead it appears to involve formation of a stable thioglycoside. Facile cross-linking was also observed with the protease papain, which like AGT has a low pKa cysteine, and the tripeptide glutathione.

Dinuclear gold(I) Complexes with Bidentate NHC Ligands as Precursors for Alkynyl Complexes via Mechanochemistry.

The use of alkynyl gold(I) complexes covers different research fields, such as bioinorganic chemistry, catalysis, and material science, considering the luminescent properties of the complexes. Regarding this last application, we report here the synthesis of three novel dinuclear gold(I) complexes of the general formula [(diNHC)(Au-C≡CPh)2]: two Au-C≡CPh units are connected by a bridging di(N-heterocyclic carbene) ligand, which should favor the establishment of semi-supported aurophilic interactions. The complexes can be easily synthesized through mechanochemistry upon reacting the pristine dibromido complexes [(diNHC)(AuBr)2] with phenylacetylene and KOH. Interestingly, we were also able to isolate the monosubstituted complex [(diNHC)(Au-C≡CPh)(AuBr)]. The gold(I) species were fully characterized by multinuclear NMR spectroscopy and mass spectrometry. The emission properties were also evaluated, and the salient data are comparable to those of analogous compounds reported in the literature.

Carbon Isotope Fractionation of 1,2-Dibromoethane by Biological and Abiotic Processes.

1,2-Dibromethane (EDB) is a toxic fuel additive that likely occurs at many sites where leaded fuels have impacted groundwater. This study quantified carbon (C) isotope fractionation of EDB associated with anaerobic and aerobic biodegradation, abiotic degradation by iron sulfides, and abiotic hydrolysis. These processes likely contribute to EDB degradation in source zones (biodegradation) and in more dilute plumes (hydrolysis). Mixed anaerobic cultures containing dehalogenating organisms (e.g., Dehaloccoides spp.) were examined, as were aerobic cultures that degrade EDB cometabolically. Bulk C isotope enrichment factors (εbulk) associated with biological degradation covered a large range, with mixed anaerobic cultures fractionating more (εbulk from -8 to -20‰) than aerobic cultures (εbulk from -3 to -6‰). εbulk magnitudes associated with the abiotic processes (dihaloelimination by FeS/FeS2 and hydrolysis) were large but fairly well constrained (εbulk from -19 to -29‰). As expected, oxidative mechanisms fractionated EDB less than dihaloelimination and substitution mechanisms, and biological systems exhibited a larger range of fractionation, potentially due to isotope masking effects. In addition to quantifying and discussing εbulk values, which are highly relevant for quantifying in situ EDB degradation, an innovative approach for constraining the age of EDB in the aqueous phase, based on fractionation during hydrolysis, is described.

Formation of S-[2-(N6-Deoxyadenosinyl)ethyl]glutathione in DNA and Replication Past the Adduct by Translesion DNA Polymerases.

1,2-Dibromoethane (DBE, ethylene dibromide) is a potent carcinogen due at least in part to its DNA cross-linking effects. DBE cross-links glutathione (GSH) to DNA, notably to sites on 2'-deoxyadenosine and 2'-deoxyguanosine ( Cmarik , J. L. , et al. ( 1991 ) J. Biol. Chem. 267 , 6672 - 6679 ). Adduction at the N6 position of 2'-deoxyadenosine (dA) had not been detected, but this is a site for the linkage of O6-alkylguanine DNA alkyltransferase ( Chowdhury , G. , et al. ( 2013 ) Angew. Chem. Int. Ed. 52 , 12879 - 12882 ). We identified and quantified a new adduct, S-[2-(N6-deoxyadenosinyl)ethyl]GSH, in calf thymus DNA using LC-MS/MS. Replication studies were performed in duplex oligonucleotides containing this adduct with human DNA polymerases (hPols) η, ι, and κ, as well as with Sulfolobus solfataricus Dpo4, Escherichia coli polymerase I Klenow fragment, and bacteriophage T7 polymerase. hPols η and ι, Dpo4, and Klenow fragment were able to bypass the adduct with only slight impedance; hPol η and ι showed increased misincorporation opposite the adduct compared to that of unmodified 2'-deoxyadenosine. LC-MS/MS analysis of full-length primer extension products by hPol η confirmed the incorporation of dC opposite S-[2-(N6-deoxyadenosinyl)ethyl]GSH and also showed the production of a -1 frameshift. These results reveal the significance of N6-dA GSH-DBE adducts in blocking replication, as well as producing mutations, by human translesion synthesis DNA polymerases.

Development of an inhalation unit risk factor for ethylene dibromide.

The Texas Commission on Environmental Quality (TCEQ) follows standard scientific methods to develop up-to-date toxicity factors for chemicals emitted in the state of Texas. An inhalation unit risk factor (URF) was developed for ethylene dibromide (EDB, CAS 106-93-4) based on an increased incidence of nasal cavity adenocarcinomas observed in female rats in a 2-year inhalation cancer bioassay conducted by the National Toxicology Program (NTP). The NTP study provided evidence of several EDB-induced tumors in male and female rats and in female mice. Tumor incidences that were statistically increased at the low dose and that showed a statistically significant increasing trend were considered in identifying the critical effect. Following benchmark concentration (BMC) modeling and animal-to-human dosimetric adjustments, the increased incidence of nasal cavity adenocarcinomas observed in female rats was determined to be the most sensitive tumorigenic effect in the most sensitive species and sex and was utilized as the carcinogenic endpoint for the development of the URF. The 95% lower confidence limit of the BMC at the 10% excess risk level (BMCL10 of 292.8 ppb) was determined for calculation of the URF. The resulting URF based on increased nasal cavity adenocarcinomas observed in female rats is 3.4E-04 per ppb (4.4E-05 per µg/m3). The lifetime air concentration corresponding to a no significant excess risk level of one in 100,000 is 0.029 ppb (0.22 µg/m3), which is considered sufficiently health-protective for use in protecting the general public against the potential carcinogenic effects of chronic exposure to EDB in ambient air.

Dual Carbon-Bromine Stable Isotope Analysis Allows Distinguishing Transformation Pathways of Ethylene Dibromide.

The present study investigated dual carbon-bromine isotope fractionation of the common groundwater contaminant ethylene dibromide (EDB) during chemical and biological transformations, including aerobic and anaerobic biodegradation, alkaline hydrolysis, Fenton-like degradation, debromination by Zn(0) and reduced corrinoids. Significantly different correlation of carbon and bromine isotope fractionation (ΛC/Br) was observed not only for the processes following different transformation pathways, but also for abiotic and biotic processes with, the presumed, same formal chemical degradation mechanism. The studied processes resulted in a wide range of ΛC/Br values: ΛC/Br = 30.1 was observed for hydrolysis of EDB in alkaline solution; ΛC/Br between 4.2 and 5.3 were determined for dibromoelimination pathway with reduced corrinoids and Zn(0) particles; EDB biodegradation by Ancylobacter aquaticus and Sulfurospirillum multivorans resulted in ΛC/Br = 10.7 and 2.4, respectively; Fenton-like degradation resulted in carbon isotope fractionation only, leading to ΛC/Br ∞. Calculated carbon apparent kinetic isotope effects ((13)C-AKIE) fell with 1.005 to 1.035 within expected ranges according to the theoretical KIE, however, biotic transformations resulted in weaker carbon isotope effects than respective abiotic transformations. Relatively large bromine isotope effects with (81)Br-AKIE of 1.0012-1.002 and 1.0021-1.004 were observed for nucleophilic substitution and dibromoelimination, respectively, and reveal so far underestimated strong bromine isotope effects.

A four-component reaction of aryldiazonium tetrafluoroborates, sulfur dioxide, 1,2-dibromoethane, and hydrazines.

A four-component reaction of aryldiazonium tetrafluoroborates, sulfur dioxide, 1,2-dibromoethane, and hydrazines under metal-free conditions is described, providing a novel and efficient approach to 2-arylsulfonyl hydrazones. This transformation proceeds smoothly via insertion of sulfur dioxide under mild conditions with good functional group tolerance.

Biodegradation of low concentrations of 1,2-dibromoethane in groundwater is enhanced by phenol.

The lead scavenger 1,2-dibromoethane (EDB), a former additive to leaded gasoline, is a common groundwater contaminant, yet not much knowledge is available for its targeted bioremediation, especially under in situ conditions. The study site was an aviation gas spill site, which, although all hydrocarbons and most of the EDB were remediated in the mid-1990s, still exhibits low levels of EDB remaining in the groundwater (about 11 µg EDB/l). To evaluate the effect of phenol on biostimulation of low concentration of EDB, microcosms were established from an EDB-contaminated aquifer. After 300 days at environmentally relevant conditions (12 ± 2 °C, static incubation), EDB was not significantly removed from unamended microcosms compared to the abiotic control. However, in treatments amended with phenol, up to 80 % of the initial EDB concentration had been degraded, while added phenol was removed completely. Microbial community composition in unamended and phenol-amended microcosms remained unchanged, and Polaromonas sp. dominated both types of microcosms, but total bacterial abundance and numbers of the gene for phenol hydroxylase were higher in phenol-amended microcosms. Dehalogenase, an indicator suggesting targeted aerobic biodegradation of EDB, was not detected in either treatment. This finding suggests phenol hydroxylase, rather than a dehalogenation reaction, may be responsible for 1,2-dibromoethane oxidation under in situ conditions. In addition, biostimulation of EDB is possible through the addition of low levels of phenol in aerobic groundwater sites.

Kinetics of 1,2-dichloroethane and 1,2-dibromoethane biodegradation in anaerobic enrichment cultures.

1,2-Dichloroethane (1,2-DCA) and 1,2-dibromoethane (ethylene dibromide [EDB]) contaminate groundwater at many hazardous waste sites. The objectives of this study were to measure yields, maximum specific growth rates (µ), and half-saturation coefficients (K(S)) in enrichment cultures that use 1,2-DCA and EDB as terminal electron acceptors and lactate as the electron donor and to evaluate if the presence of EDB has an effect on the kinetics of 1,2-DCA dehalogenation and vice versa. Biodegradation was evaluated at the high concentrations found at some industrial sites (>10 mg/liter) and at lower concentrations found at former leaded-gasoline sites (1.9 to 3.7 mg/liter). At higher concentrations, the Dehalococcoides yield was 1 order of magnitude higher when bacteria were grown with 1,2-DCA than when they were grown with EDB, while µ's were similar for the two compounds, ranging from 0.19 to 0.52 day(-1) with 1,2-DCA to 0.28 to 0.36 day(-1) for EDB. K(S) was larger for 1,2-DCA (15 to 25 mg/liter) than for EDB (1.8 to 3.7 mg/liter). In treatments that received both compounds, EDB was always consumed first and adversely impacted the kinetics of 1,2-DCA utilization. Furthermore, 1,2-DCA dechlorination was interrupted by the addition of EDB at a concentration 100 times lower than that of the remaining 1,2-DCA; use of 1,2-DCA did not resume until the EDB level decreased close to its maximum contaminant level (MCL). In lower-concentration experiments, the preferential consumption of EDB over 1,2-DCA was confirmed; both compounds were eventually dehalogenated to their respective MCLs (5 µg/liter for 1,2-DCA, 0.05 µg/liter for EDB). The enrichment culture grown with 1,2-DCA has the advantage of a more rapid transition to 1,2-DCA after EDB is consumed.

In vivo roles of conjugation with glutathione and O6-alkylguanine DNA-alkyltransferase in the mutagenicity of the bis-electrophiles 1,2-dibromoethane and 1,2,3,4-diepoxybutane in mice.

Several studies with bacteria and in vitro mammalian systems have provided evidence of the roles of two thiol-based conjugation systems, glutathione (GSH) transferase and O(6)-alkylguanine DNA-alkyltransferase (AGT), in the bioactivation of the bis-electrophiles 1,2-dibromoethane and 1,2,3,4-diepoxybutane (DEB), the latter an oxidation product of 1,3-butadiene. The in vivo relevance of these conjugation reactions to biological activity in mammals has not been addressed, particularly with DEB. In this work, we used transgenic Big Blue mice, utilizing the cII gene, to examine the effects of manipulation of conjugation pathways on liver mutations arising from dibromoethane and DEB in vivo. Treatment of the mice with butathionine sulfoxime (BSO) prior to dibromoethane lowered hepatic GSH levels, dibromoethane-GSH DNA adduct levels (N(7)-guanyl), and the cII mutation frequency. Administration of O(6)-benzylguanine (O(6)-BzGua), an inhibitor of AGT, did not change the mutation frequency. Depletion of GSH (BSO) and AGT (O(6)-BzGua) lowered the mutation frequency induced by DEB, and BSO lowered the levels of GSH-DEB N(7)-guanyl and N(6)-adenyl DNA adducts. Our results provide evidence that the GSH conjugation pathway is a major in vivo factor in dibromoethane genotoxicity; both GSH conjugation and AGT conjugation are major factors in the genotoxicity of DEB. The latter findings are considered to be relevant to the carcinogenicity of 1,3-butadiene.

Differences in crystallization of two LinB variants from Sphingobium japonicum UT26.

Haloalkane dehalogenases are microbial enzymes that convert a broad range of halogenated aliphatic compounds to their corresponding alcohols by the hydrolytic mechanism. These enzymes play an important role in the biodegradation of various environmental pollutants. Haloalkane dehalogenase LinB isolated from a soil bacterium Sphingobium japonicum UT26 has a relatively broad substrate specificity and can be applied in bioremediation and biosensing of environmental pollutants. The LinB variants presented here, LinB32 and LinB70, were constructed with the goal of studying the effect of mutations on enzyme functionality. In the case of LinB32 (L117W), the introduced mutation leads to blocking of the main tunnel connecting the deeply buried active site with the surrounding solvent. The other variant, LinB70 (L44I, H107Q), has the second halide-binding site in a position analogous to that in the related haloalkane dehalogenase DbeA from Bradyrhizobium elkanii USDA94. Both LinB variants were successfully crystallized and full data sets were collected for native enzymes as well as their complexes with the substrates 1,2-dibromoethane (LinB32) and 1-bromobutane (LinB70) to resolutions ranging from 1.6 to 2.8 Å. The two mutants crystallize differently from each other, which suggests that the mutations, although deep inside the molecule, can still affect the protein crystallizability.

On the sensitivity of hard X-ray spectroscopies to the chemical state of Br.

The sensitivity of the 1s X-ray emission and high-energy-resolution fluorescence-detected X-ray absorption spectroscopies (XES and HERFD-XAS) to resolve the variations in the chemical state (electronic structure and local coordination) of Br has been investigated for a selected set of compounds including NaBrO3, NH4Br and C2H4Br2 (1,2-dibromoethane). For the Br K-edge XAS, employing the HERFD mode significantly increases the energy resolution, which demonstrates that with a crystal spectrometer used as a detector the absorption technique becomes a more powerful analytical tool. In the case of XES, the experimental results as well as the density functional theory (DFT) modeling both show that the chemical sensitivity of the main 1s diagram emission lines (Kα1,2 and Kß1,3) is rather limited. However, the valence-to-core (Kß2) region of XES displays significant shape and intensity variations, as expected for transitions having the same final states as those of photoemission spectroscopy. The spectra are in good agreement with the molecular orbital description delivered by DFT calculations. Calculations for an extended series of Br compounds confirm that valence-to-core XES can serve as a probe for chemical analysis, and, being a hard X-ray photon-in/photon-out technique, it is particularly well-suited for in situ investigations of molecular transformations, even on the ultrafast time scales down to femtosecond time resolution.

Case of the missing isomer: pathways for molecular elimination in the photoinduced decomposition of 1,1-dibromoethane.

We report an experimental and computational study of the photodecomposition pathways of a prototypical gem-dihalide, 1,1-dibromoethane (1,1-EDB), in the condensed phase. Following photolysis of the matrix isolated parent compound in Ar at 5 K, photoproducts are observed corresponding to Br2 elimination (+ C2H4 or C2H2) and HBr elimination (+ vinyl bromide). The elimination products are observed in the matrix as complexes. In contrast to our recent studies of the photolysis of matrix isolated polyhalomethanes, no evidence for the iso-1,1-EDB species is found, although studies of the matrix isolated 1,1-dibromo-2,2,2-trifluoroethane analogue show that the isomer is the dominant photoproduct. These results are examined in the light of theoretical studies that have characterized in detail the 1,1-EDB potential energy surface (PES). For Br2 elimination, a pathway from the isomer on the singlet PES is found which involves a simultaneous Br2 loss with 1,2-hydrogen shift; this pathway lies lower in energy than a concerted three-center elimination from the parent 1,1-EDB. For HBr elimination, our previous theoretical studies [Kalume, A.; George, L.; Cunningham, N.; Reid, S. A. Chem. Phys. Lett. 2013, 556, 35-38] have demonstrated the existence of concerted (single-step) and sequential pathways that involve coupled proton and electron transfer, with the sequential pathway involving the isomer as an intermediate. Here, more extensive computational results argue against a simple radical abstraction pathway for this process, and we compare experimental and computational results to prior results from the photolysis of the structural isomer, 1,2-EDB. These steady-state experiments set the stage for ultrafast studies of the dynamics of this system, which will be important in unraveling the complex photodecomposition pathways operative in condensed phases.

Therapeutic plasma exchange: an effective treatment in ethylene dibromide poisoning cases.

BACKGROUND: Ethylene dibromide (EDB) poisoning is very common in Central India and has fatal outcome. EDB is highly protein bound and, therefore, it is suggested that therapeutic plasma exchange (TPE) may be useful in removing drug from body shortly after ingestion before EDB metabolizes and causes severe end organ damage. The aim of our study is to find the effect of time of start of TPE on survival outcome of EDB poisoning cases. MATERIAL AND METHODS: Fifty-eight cases of EDB poisoning were reviewed from 2007 to 2012 in Department of critical care medicine in tertiary care hospitals at Indore. Five patients were discharged against medical advice and lost to follow up. TPE was done in 47 patients as early as possible and irrespective of appearance of clinical symptoms. TPE was not performed in six cases as they were hypotensive at admission. RESULT: The patients with EDB poisoning were 15-45 yrs old with 3:2 male to female ratio. Out of 47 who received TPE, 39 patients survived. TPE had started within 24 h of ingestions of EDB in 36 out of 39 survived patients. Survival outcome was nine times higher in patients who received TPE within 24 h than after 24 h of ingestion. Survival rate was increased to 100% in patients where TPE was done within 12 h of ingestion of EDB. CONCLUSION: Early TPE help to remove plasma protein bound toxin with significant mortality reduction. However, delay in start of TPE after ingestion of poison has significant poor survival outcome.

Carbon isotope fractionation in reactions of 1,2-dibromoethane with FeS and hydrogen sulfide.

EDB (1,2-dibromoethane) is frequently detected at sites impacted by leaded gasoline. In reducing environments, EDB is highly susceptible to abiotic degradation. A study was conducted to evaluate the potential of compound-specific isotope analysis (CSIA) in assessing abiotic degradation of EDB in sulfate-reducing environments. Water containing EDB was incubated in sealed vials with various combinations of Na(2)S (<0.7 mM) and mackinawite (FeS) (180 mM). Degradation rates in vials containing FeS exceeded those in Na(2)S-only controls. In the presence of FeS, first-order constants ranged from 0.034 ± 0.002 d(-1) at pH 6 to 0.081 ± 0.005 d(-1) at pH 8.5. In the presence of FeS, products from reductive debromination (ethylene) and from S(N)2 substitution with S(II) nucleophiles were detected (1,2-dithioethane, DTA). Relatively high yields of DTA suggested that the S(N)2 reactions were not mediated by HS(-) only but likely also included reactions mediated by FeS surface. Significant carbon isotope effects were observed for nucleophilic substitution by HS(-) (ε = -31.6 ± 3.7‰) and for a combination of reductive and substitution pathways in the presence of FeS (-30.9 ± 0.7‰), indicating good site assessment potential of CSIA. The isotope effects (KIEs) observed in the presence of FeS corroborated the predominance of S(N)2 substitution by nucleophiles combined with two-electron transfer reductive debromination.

Facile charge-displacement at silicon gives spaced-out reaction.

Adsorbates on metals, but not previously on semiconductors, have been observed to display long-range repulsive interactions. On metals, due to efficient dissipation, the repulsions are weak, typically on the order of 5 meV at 10 Å. On the 7×7 reconstruction of the Si(111) surface, charge transport through the surface has been demonstrated by others using charge injection by STM tips. Here we show that for both physisorbed brominated molecules, and for chemisorbed Br-atoms, induced charge-transfer in the Si(111)-7×7 surface can lead to a strong repulsive interaction between adsorbates, calculated as 200 meV at 13.4 Å. This large repulsive interaction must be channeled through the surface since it causes widely spaced "one-per-corner-hole" patterns of physisorption (three cases--directly observed here) and subsequent chemisorption (four cases observed). The patterns were observed by ultrahigh vacuum scanning tunneling microscopy for four different brominated hydrocarbon adsorbates; 1,2-dibromoethane, 1-bromopropane, 1-bromopentane, and bromobenzene, deposited individually on the surface. In every case, adsorbates were overwhelmingly more likely to be found singly than multiply adjacent to a corner-hole, constituting a distinctive pattern having a probability p = 7 × 10(-5) compared to a random distribution.

Simulation of Ligand Transport in Receptors Using CaverDock.

Interactions between enzymes and small molecules lie in the center of many fundamental biochemical processes. Their analysis using molecular dynamics simulations have high computational demands, geometric approaches fail to consider chemical forces, and molecular docking offers only static information. Recently, we proposed to combine molecular docking and geometric approaches in an application called CaverDock. CaverDock is discretizing enzyme tunnel into discs, iteratively docking with restraints into one disc after another and searching for a trajectory of the ligand passing through the tunnel. Here, we focus on the practical side of its usage describing the whole method: from getting the application, and processing the data through a workflow, to interpreting the results. Moreover, we shared the best practices, recommended how to solve the most common issues, and demonstrated its application on three use cases.

[Design and synthesis of novel PPARgamma agonists].

OBJECTIVE: To design and synthesize novel peroxisome proliferator-activated receptor gamma (PPARgamma) agonists. METHODS: A series of novel PPARgamma agonists were designed based on the binding character of PPARgamma agonists and the distribution of pharmacophore. The target compounds were synthesized using p-hydroxybenzaldehyde, 1, 2-dibromoethane, phenol, hydantoin and 2-thiohydantoin as materials. RESULTS: Twelve compounds were synthesized by etherification and Knoevenagle condensation. CONCLUSION: The target compounds were efficiently synthesized under mild condition and the structures of the target compounds were confirmed by 1HNMR and MS.