Carcinogenesis of Urethane: Simulation versus Experiment

Abstract

The carcinogenesis of urethane (ethyl carbamate), a by-product of fermentation that is consistently found in various food products, was investigated with a combination of kinetic experiments and quantum chemical calculations. The main objective of the study was to find ΔG‡, the activation free energy for the rate-limiting step of the SN2 reaction between the ultimate carcinogen of urethane, vinyl carbamate epoxide (VCE), and different nucleobases of the DNA. In the experimental part, the second-order reaction rate constants for the formation of the main 7-(2-oxoethyl)guanine adduct in aqueous solution of deoxyguanosine and in DNA were determined. A series of ab initio, density functional theory (DFT) and semiempirical molecular orbital (MO) calculations was then performed to determine the activation barriers for the reaction between VCE and nucleobases methylguanine, methyladenine, and methylcytosine. Effects of hydration were incorporated with the use of the solvent reaction field method of Tomasi and co-workers and the Langevine dipoles model of Florian and Warshel. The computational results for the main adduct were found to be in good agreement with the experiment, thus presenting a strong evidence for the validity of the proposed SN2 mechanism. This allowed us to predict the activation barriers of reactions leading to side products for which kinetic experiments have not yet been performed. Our calculations have shown that the main 7-(2-oxoethyl)deoxyguanosine adduct indeed forms preferentially because the emergence of other adducts either proceeds across a significantly higher activation barrier or the geometry of the reaction requires the Watson–Crick pairs of the DNA to be broken. The computational study also considered the questions of stereoselectivity, the ease of the elimination of the leaving group, and the relative contributions of the two possible reaction paths for the formation of the 1,N2-ethenoguanosine adduct.

Protective Effects of [6]-Gingerol Against Chemical Carcinogens: Mechanistic Insights

“…The Hartree−Fock (HF) level of theory, combined with flexible 6-311++G(d,p) basis set and implicit solvation model, was found to give a very good agreement with the experimental activation free energies for the alkylation reactions between all nine studied ultimate chemical carcinogens and the most reactive DNA base guanine [1,7,12,13,16]. Moreover, an observation has been reported in the scientific literature, that both the B3LYP density functional and the MP2 theory levels, which include a certain degree of dynamical electron correlation, exhibit moderate to significant underestimation of the experimental ∆G ‡ regardless of the applied solvation model [1,7,12,13,16]. Hartree-Fock level of theory also provides a strong argument in favor of the proposed S N 2 reaction mechanism for guanine alkylation by these chemical carcinogens.…”

“…Hartree-Fock level of theory also provides a strong argument in favor of the proposed S N 2 reaction mechanism for guanine alkylation by these chemical carcinogens. Moreover, it represents a good confirmation of the applicability of quantum chemical simulations to alkylation reactions related to carcinogenesis [12,16]. This encouraged us to employ the Hartree-Fock method with three different flexible basis sets to predict the activation barriers of chemical reactions involving the nine ultimate carcinogens and two natural scavengers, namely [6]-gingerol and glutathione, for which kinetic experiments have not been performed yet.…”

“…where k B represents the Boltzmann constant, h the Planck constant, T the thermodynamic temperature, and ∆G ‡ the activation free energy. Transition state theory is based on the assumption that reactants and transition states form a thermal equilibrium [16]. Quantum-mechanical calculations were carried out on the CROW cluster located at the National Institute of Chemistry in Ljubljana [41].…”

“…As the examined alkylation reactions take place in a solution, the values of ∆E ‡ , which are calculated in vacuo, cannot be readily compared to the experimental results of kinetic studies [16]. Therefore, we performed a series of calculations where implicit solvation effects were incorporated.…”

Carbonyl compounds in wine: factors related to presence and toxic effects

“…EC toxicity is connected to its metabolization into vinyl carbamate epoxide via cytochrome P450 2E1, especially in liver. This electrophilic specie can bind covalently to the DNA forming an adduct; and therefore, has mutagenic and carcinogenic potential (LAJOVIC et al, 2015). The generation of ROS has also been related to exposure to EC, triggering oxidative stress and cell death via energy depletion and disruption of cells membrane integrity (LIU et al, 2017).…”