TY - JOUR A1 - Durmaz, V. A1 - Weber, M. A1 - Becker, Roland T1 - How to simulate affinities for host-guest systems lacking binding mode information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers N2 - A novel approach for the simulation of host.guest systems by systematically scanning the host moleculefs orientations within the guest cavity is presented along with a thermodynamic strategy for determining preferential binding modes and corresponding optimal interaction energies between host and guest molecules. By way of example, the elution order of hexabromocyclododecane stereoisomers from high performance liquid chromatography separation on a permethylated β-cyclcodextrin stationary phase has been computed using classical molecular dynamics simulations with the explicit solvents water and acetonitrile. Comparison of estimated with experimental separation data reveals remarkable squared coefficients of correlation with R2=0.87 and a very high correlation RLOO2 . 0:72 using the leaveone-out cross-validation method and water as solvent. In particular, the approach presented shapes up as very robust in terms of the evaluated time range under consideration, reflecting well thermodynamic equilibria. These and further observations correlating with experimental results suggest the suitability of the underlying force fields and our multi-mode approach for the estimation of relative binding affinities for host–guest systems with unknown binding modes. KW - Molecular simulation KW - Molecular dynamics KW - Binding affinity KW - Elution order KW - Beta-cyclodextrin PY - 2012 DO - https://doi.org/10.1007/s00894-011-1239-5 SN - 1610-2940 SN - 0948-5023 VL - 18 IS - 6 SP - 2399 EP - 2408 PB - Springer CY - Berlin; Heidelberg AN - OPUS4-26112 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Scharkoi, O. A1 - Esslinger, Susanne A1 - Becker, Roland A1 - Weber, M. A1 - Nehls, Irene T1 - Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the steroisomerism of hydroxylated metabolites T2 - DIOXIN 2011 CY - Brussels, Belgium DA - 2011-08-21 KW - Bromierte Falmmschutzmittel KW - Hexabromcyclododecan KW - Cytochrom KW - Metaboliten KW - HPLC KW - Simulation PY - 2011 UR - http://www.dioxin20xx.org/pdfs/2011/1810.pdf SN - 1026-4892 VL - 73 SP - 730 EP - 733 AN - OPUS4-27263 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Weber, M. A1 - Durmaz, V. A1 - Becker, Roland A1 - Esslinger, Susanne T1 - Predictive identification of Pentabromocyclododecene (PBCD) isomers with high binding affinity to hTTR N2 - The binding affinities of the six main hexabromocyclododecane (HBCD) stereoisomers and all of their possible 48 allylic pentabromocyclododecene (PBCD) metabolites to the endocrinous human transthyretin receptor (hTTR) were investigated and compared to the natural binder thyroxine, and the two brominated diphenyl ethers BDE-47 and 3-hydroxy-BDE-47. The endocrine disrupting potency was approximated by a combination of two methods: a surface matching with the natural binder thyroxine (T4) followed by approximation of free binding energies for various binding modes within hTTR. The results indicate slightly higher binding affinities for both BDE structures than for T4 itself and similarly high affinities for two trans-configurated PBCD isomers. For many other PBCD isomers, intermediate values were computed, whereas all HBCD diastereomers yielded significantly lower binding affinities. T2 - Dioxin 2009 - 29th International symposium on halogenated persistent organic pollutants / Organohalogen compounds CY - Beijing, China DA - 2009-08-23 KW - Flammschutzmittel KW - Thyroxin KW - Molecular modeling PY - 2009 UR - http://www.dioxin20xx.org/pdfs/2009/09-54.pdf VL - 71 SP - 000247 EP - 000252 CY - Beijing, China AN - OPUS4-20980 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Scharkoi, O. A1 - Becker, Roland A1 - Esslinger, Susanne A1 - Weber, M. A1 - Nehls, Irene T1 - Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane N2 - This article describes a simple and quick in silico method for the prediction of cytochrome P450 (CYP)-mediated hydroxylation of drug-like compounds. Testosterone and progesterone, two known substrates of CYP3A4, are used to test the method. Further, we apply the procedure to predict sites of hydroxylation of isomers of the flame retardant hexabromocyclododecane by CYP3A4. Within the method, the compound is rotated in the binding pocket of the cytochrome, so that each hydrogen under consideration is placed near the active centre. Afterwards, short molecular dynamics simulations are provided for each step of the rotation. All steps of the simulation are compared concerning the distances between the hydrogens and the active centre and the corresponding energies. The computational results correlate well with experimental results. KW - Predicting sites of metabolism KW - Cytochrome P450 KW - Hydroxylation KW - Metabolism of HBCD PY - 2015 DO - https://doi.org/10.1080/08927022.2014.898845 SN - 0892-7022 SN - 1029-0435 VL - 41 IS - 7 SP - 538 EP - 546 PB - Gordon and Breach CY - New York, NY AN - OPUS4-30492 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Weber, M. A1 - Becker, Roland A1 - Köppen, Robert A1 - Durmaz, V. T1 - Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane N2 - In this paper, we investigate the interconversion processes of the major flame retardant - 1,2,5,6,9,10-hexabromocyclododecane (HBCD) - by the means of statistical thermodynamics based on classical force-fields. Three ideas will be presented. First, the application of classical hybrid Monte-Carlo simulations for quantum mechanical processes will be justified. Second, the problem of insufficient convergence properties of hybrid Monte-Carlo methods for the generation of low temperature canonical ensembles will be solved by an interpolation approach. Furthermore, it will be shown how free energy differences can be used for a rate matrix computation. The results of our numerical simulations will be compared to experimental results. KW - Markov process KW - Molecular dynamics KW - Rate matrix PY - 2007 SN - 1438-0064 VL - 07-31 SP - 1 EP - 18 PB - ZIB CY - Berlin AN - OPUS4-17841 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Weber, M. A1 - Becker, Roland A1 - Durmaz, V. A1 - Köppen, Robert T1 - Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers KW - HBCD KW - Isomerisation KW - Statistical thermodynamics KW - Kinetics PY - 2008 DO - https://doi.org/10.1080/08927020802208968 SN - 0892-7022 SN - 1029-0435 VL - 34 IS - 6-7 SP - 727 EP - 736 PB - Gordon and Breach CY - New York, NY AN - OPUS4-18261 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Köppen, Robert A1 - Becker, Roland A1 - Weber, M. A1 - Durmaz, V. A1 - Nehls, Irene T1 - HBCD stereoisomers: Thermal interconversion and enantiospecific trace analysis in biota T2 - DIOXIN 2008, 28th International Symposium on Halogenated Persistent Organic Pollutants (POPs) CY - Birmingham, UK DA - 2008-08-17 KW - HBCD KW - Stereoisomerie KW - Persistent Organic Pollutant KW - HPLC-MS PY - 2008 UR - http://www.dioxin20xx.org/pdfs/2008/08-819.pdf IS - Paper #154 SP - 1 EP - 4 AN - OPUS4-17842 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -