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.

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.

Differentiating and Quantifying Gas-Phase Conformational Isomers Using Coulomb Explosion Imaging

Conformational isomerism plays a crucial role in defining the physical and chemical properties and biological activity of molecules ranging from simple organic compounds to complex biopolymers. However, it is often a significant challenge to differentiate and separate these isomers experimentally as they can easily interconvert due to their low rotational energy barrier. Here, we use the momentum correlation of fragment ions produced after inner-shell photoionization to distinguish conformational isomers of 1,2-dibromoethane (C₂H₄Br₂). We demonstrate that the three-body breakup channel, C₂H₄⁺ + Br⁺ + Br⁺, contains signatures of both sequential and concerted breakup, which are decoupled to distinguish the geometries of two conformational isomers and to quantify their relative abundance. The sensitivity of our method to quantify these yields is established by measuring the relative abundance change with sample temperature, which agrees well with calculations. Our study paves the way for using Coulomb explosion imaging to track subtle molecular structural changes.

Simulation of dual carbon-bromine stable isotope fractionation during 1,2-dibromoethane degradation

We performed a model-based investigation to simultaneously predict the evolution of concentration, as well as stable carbon and bromine isotope fractionation during 1,2-dibromoethane (EDB, ethylene dibromide) transformation in a closed system. The modelling approach considers bond-cleavage mechanisms during different reactions and allows evaluating dual carbon-bromine isotopic signals for chemical and biotic reactions, including aerobic and anaerobic biological transformation, dibromoelimination by Zn(0) and alkaline hydrolysis. The proposed model allowed us to accurately simulate the evolution of concentrations and isotope data observed in a previous laboratory study and to successfully identify different reaction pathways. Furthermore, we illustrated the model capabilities in degradation scenarios involving complex reaction systems. Specifically, we examined (i) the case of sequential multistep transformation of EDB and the isotopic evolution of the parent compound, the intermediate and the reaction product and (ii) the case of parallel competing abiotic pathways of EDB transformation in alkaline solution.

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.

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.

[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.

Ortho effects on the change in electronic absorption spectrum of pyridinium salts of saturated bromohydrocarbon

The quaterisation process of 1,2-dibromoethane and pyridine is in situ traced by electronic absorption spectrum. Two absorption peaks, induced by mono- and bis-pyridinium salt of 1,2-dibromoethane, appear at 429 nm and 313 nm, respectively. To explain the phenomena, several kinds of alkyl bromides with special structures were selected and compared by experimental measurement and theoretical calculation. The results indicate that for mono-pyridinium salt of 1,2-dibromoethane, the electron donor property of ortho-bromine group increases the electron cloud density of the carbon atom associated with pyridinium cation, which induces red-shift of absorption wavelength.

A matrix isolation study of the photochemically induced reactions of nitrogen dioxide with 1,2-dibromoethene and 1,2-dichloroethene using Fourier transform infrared spectroscopy

Photolyses of matrices of either BrCHCHBr/NO2/Ar or ClCHCHCl/NO2/Ar using quartz-filtered radiation (lambda>240 nm) led to the appearance of infrared bands attributable to carbonyl, carbon monoxide, and ketene species; no bands belonging to a precursor complex NO2cdots, three dots, centeredXCHCHX (where X=Br or Cl) were observed upon matrix deposition. The possible reaction pathway is discussed.

1,2-Dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 degrees C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(-) [G(-)], with a refined torsion angle phi(BrCCBr)=-71(6) degrees, anti [A], with a torsion angle phi(BrCCBr) approximately -170 degrees , and gauche(+) [G(+)], with a torsion angle phi(BrCCBr) approximately +70 degrees . The second torsion angle of importance, the rotation about the CSi bond, has been refined to a value of +175(13) degrees . Torsion angles were only refined for the more abundant G(-) conformer. In the solid phase, only the G(-) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, DeltaS. The obtained composition from GED refinements was (%) G(-)/A/G(+)=64(27)/23(13)/13(18) (values with estimated 2sigma uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(-) values with estimated 2sigma uncertainties): bond lengths (r(g)):r(C-C)=1.501(18)A, r(SiC)=1.865(15)A, r(CBr)=1.965(8)A (average), r(SiCl)=2.028(3)A (average). Bond angles ( anglealpha):angleCCSi=114.1(33) degrees , angleC1C2Br=114.0(21) degrees , angleCSiCl=109.6(7) degrees (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.

Extractive Phase Vanishing Reactions with Dichloromethane, Perfluorohexanes, and Dibromoethane: Slow Addition in a Test Tube

[reaction: see text] Partition coefficient measurements and experiments with a dye show that a new fluorous "phase vanishing reaction" described by Jana and Verkade occurs by an extractive mechanism. This mechanism is contrasted with the original diffusive phase-vanishing reactions introduced by Ryu and co-workers.

Characterization of a mutagenic DNA adduct formed from 1,2-dibromoethane by O6-alkylguanine-DNA alkyltransferase

It has been proposed that the DNA repair protein O6-alkylguanine-DNA alkyltransferase increases the mutagenicity of 1,2-dibromoethane by reacting with it at its cysteine acceptor site to form a highly reactive half-mustard, which can then react with DNA (Liu, L., Pegg, A. E., Williams, K. M., and Guengerich, F. P. (2002) J. Biol. Chem. 277, 37920-37928). Incubation of Escherichia coli-expressed human alkyltransferase with 1,2-dibromoethane and single-stranded oligodeoxyribonucleotides led to the formation of covalent transferaseoligo complexes. The order of reaction determined was Gua>Thy>Cyt>Ade. Mass spectrometry analysis of the tryptic digest of the reaction product indicated that some of the adducts led to depurination with the release of the Gly136-Arg147 peptide cross-linked to a Gua at the N7 position, with the site of reaction being the active site Cys145 as established by chromatographic retention time and the fragmentation pattern determined by tandem mass spectrometry of a synthetic peptide adduct. The alkyltransferase-mediated mutations produced by 1,2-dibromoethane were predominantly Gua to Ade transitions but, in the spectrum of such rifampicin-resistant mutations in the RpoB gene, 20% were Gua to Thy transversions. The latter are likely to have arisen from the apurinic site generated from the Gua-N7 adduct. Support exists for an additional adduct/mutagenic pathway because evidence was obtained for DNA adducts other than at the Gua N7 atom and for mutations other than those attributable to depurination. Thus, chemical and biological evidence supports the existence of at least two alkyltransferase-dependent pathways for 1,2-dibromoethane-induced mutagenicity, one involving Gua N7-alkylation by alkyltransferase-S-CH2CH2Br and depurination, plus another as yet uncharacterized system(s).

Influence of mutations of Val226 on the catalytic rate of haloalkane dehalogenase

Haloalkane dehalogenase converts haloalkanes to their corresponding alcohols. The 3D structure, reaction mechanism and kinetic mechanism have been studied. The steady state k(cat) with 1,2-dichloroethane and 1,2-dibromoethane is limited mainly by the rate of release of the halide ion from the buried active-site cavity. During catalysis, the halogen that is cleaved off (Cl alpha) from 1,2-dichloroethane interacts with Trp125 and the Cl beta interacts with Phe172. Both these residues have van der Waals contacts with Val226. To establish the effect of these interactions on catalysis, and in an attempt to change enzyme activity without directly mutating residues involved in catalysis, we mutated Val226 to Gly, Ala and Leu. The Val226Ala and Val226Leu mutants had a 2.5-fold higher catalytic rate for 1,2-dibromoethane than the wild-type enzyme. A pre-steady state kinetic analysis of the Val226Ala mutant enzyme showed that the increase in k(cat) could be attributed to an increase in the rate of a conformational change that precedes halide release, causing a faster overall rate of halide dissociation. The k(cat) for 1,2-dichloroethane conversion was not elevated, although the rate of chloride release was also faster than in the wild-type enzyme. This was caused by a 3-fold decrease in the rate of formation of the alkyl-enzyme intermediate for 1,2-dichloroethane. Val226 seems to contribute to leaving group (Cl alpha or Br alpha) stabilization via Trp125, and can influence halide release and substrate binding via an interaction with Phe172. These studies indicate that wild-type haloalkane dehalogenase is optimized for 1,2-dichloroethane, although 1,2-dibromoethane is a better substrate.

Mutation spectrum of 2-chloroethyl methanesulfonate in Drosophila melanogaster premeiotic germ cells

The 2-chloroethyl methanesulfonate (2ClEMS)-induced alcohol dehydrogenase (Adh) null germline mutation frequency in treated Drosophila melanogaster second instar larval gonia was two orders of magnitude greater than the spontaneous mutation frequency. DNA sequence analysis of 83 Adh null mutations showed that 40 mutations of independent origin were at 23 sites in the Adh gene. The mutation spectrum contained only GC-->AT transitions with 35 mutations (87.5%) at the middle or 3' guanine. In addition, characteristics of glutathione (GSH)-mediated bioactivation were determined for 2ClEMS in vitro. Rates of GSH-mediated conjugation, catalyzed by purified rat liver glutathione-S-transferase (GST), and binding of [35S]GSH-mediated conjugation products to calf thymus DNA were determined for 2ClEMS, 1,2-dichloroethane (EDC) and 1,2-dibromoethane (EDB). The relative rates of GSH-mediated conjugation were the following: 5 mM EDB > 40 mM 2ClEMS > 40 mM EDC. A similar trend was observed for DNA binding of the [35S]GSH-mediated conjugation products when differences in mutagen concentration were considered: EDB > 2ClEMS > EDC. The ratios of DNA binding to GSH conjugation calculated for EDB, EDC and 2ClEMS were 6.8 x 10(-5), 9.3 x 10(-5) and 19.1 x 10(-5), respectively. A narrow range, less than a 3-fold difference, in the ratios of DNA binding to GSH conjugation indicates that the bioactivation of 2ClEMS is mediated by the same mechanism as EDB and EDC. Consequently, 2ClEMS, EDC and EDB may induce a specific mutation in premeiotic germ cells.

Spectroscopic and thermodynamic characterization of the interaction of N7-guanyl thioether derivatives of d(TGCTG*CAAG) with potential complements

The oligomer d(TGCTGCAAG) corresponds to a region of bacteriophage M13mp18 DNA where mutations have been found to be induced by S-(2-chloroethyl)glutathione (glutathione, GSH) [Cmarik, J. L., Humphreys, W. G., Bruner, K. L., Lloyd, R. S., Tibbetts, C., & Guengerich, F. P. (1991) J. Biol. Chem. 267, 6672-6679]. This oligomer was prepared with the central G replaced by S-(2-N7-guanylethyl)-GSH or N-acetyl-S-(2-N7-guanylethyl)Cys methyl ester; these derivatives were purified by HPLC and by affinity chromatography in the latter case. UV mixing and CD spectroscopy studies showed no evidence for preferred pairing of the S-(2-N7-guanylethyl)GSH moiety to any base other than C. UV melting studies of duplexes were performed with complementary strands containing the normal C, as well as the three mismatches (T, A, and G), across from the adducted base. Thermal stabilities were reduced in all cases when G was replaced by either N7-guanyl adduct; the C-containing complement was still the most stable. The reduced stability of the duplex d(TGCTG*CAAG)/d(CTTGCAGCA), where S-(2-N7-guanylethyl)-GSH corresponds to G*, was characterized by an increase in delta G zero of 1.4-2.0 kcal mol-1 (in the range of 25-37 degrees C) relative to the unadducted duplex. van't Hoff analysis of concentration-dependent melting experiments indicated that the delta H zero of the duplex was actually more favorable when this adduct was introduced (delta delta H zero = 13 kcal mol-1), but the decreased thermal stability was due to the entropic component. Similar results were observed when G* was N-acetyl-S-(2-N7-guanylethyl)Cys methyl ester. Under the conditions used, the overall relative stabilities of the oligomeric duplexes containing various base pairs do not indicate that S-(2-N7-guanylethyl)GSH would contribute to a higher frequency of T misinsertion than G. The possibility that ionization at the guanine N1 position may be involved in mutagenesis by N7-guanyl adducts is considered.