Carcinogenicity of benzo[a]pyrene diol epoxide stereoisomers: A linear free energy relationship study

Formation and growth mechanisms of polycyclic aromatic hydrocarbons: A mini-review

Polycyclic aromatic hydrocarbons (PAHs) are mostly formed during the incomplete combustion of organic materials, but their importance and presence in materials science, and astrochemistry has also been proven. These carcinogenic persistent organic pollutants are essential in the formation of combustion generated particles as well. Due to their significant impact on the environment and human health, to understand the formation and growth of PAHs is essential. Therefore, the most important growth mechanisms are reviewed, and presented here from the past four decades (1981-2021) to initiate discussions from a new perspective. Although, the collected and analyzed observations are derived from both experimental, and computational studies, it is neither a systematic nor a comprehensive review. Nevertheless, the mechanisms were divided into three main categories, acetylene additions (e.g. HACA), vinylacetylene additions (HAVA), and radical reactions, and discussed accordingly.

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

Non-covalent interactions of the carcinogen (+)-anti-BPDE with exon 1 of the human K-ras proto-oncogene

Investigating the complementary, but different, effects of physical (non-covalent) and chemical (covalent) mutagen-DNA and carcinogen-DNA interactions is important for understanding possible mechanisms of development and prevention of mutagenesis and carcinogenesis. A highly mutagenic and carcinogenic metabolite of the polycyclic aromatic hydrocarbon benzo[α]pyrene, namely (+)-anti-BPDE, is known to undergo both physical and chemical complexation with DNA. Previous studies of BPDE-DNA complex formation have focused on processes that require substantial structural reorganization, such as intercalation, and consequently relatively long time scales. However, some initial processes which occur within shorter time scales, such as external non-covalent binding, and which do not require major DNA structural reorganization have not been thoroughly investigated. A detailed computational study of such initial BPDE-DNA interactions is needed to elucidate the temporal and structural origins of the major covalent adduct, a promutagenic, which is known to exist in an external (+)-trans-anti-BPDE-N(2)-dGuanosine configuration. Accordingly, the initial stages of external non-covalent BPDE-DNA binding are studied in this work as well as their relationship to subsequent formation of the major, also external, covalent adduct. To study mechanisms that occur prior to extensive DNA structural reorganization, we present a first and detailed codon by codon computational study of the non-covalent interactions of (+)-anti-BPDE with DNA. In particular, due to its relevance to carcinogenesis, the interaction of (+)-anti-BPDE with exon 1 of the human K-ras gene has been studied. External solvent-exposed non-covalent binding sites have been found which may be precursors of the major external trans adduct and, importantly, are located in codons 12 and 13 of the K-ras gene which are known to be key mutation hotspots. In addition, our study explains and correctly predicts preferential (+)-anti-BPDE binding at minor groove guanosines. A subtle combination of van der Waals and hydrogen bonding interactions has been found to be a primary factor in preferentially positioning (+)-anti-BPDE toward the 5' position of a guanosine's strand, consistent with proton NMR observations for the major trans adduct, and at 5'-TGG-3' sequences which are known to yield high binding probability.

Mechanism of epoxide hydrolysis in microsolvated nucleotide bases adenine, guanine and cytosine: a DFT study

Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that hydrated DNA bases become highly S(N)2 active on epoxide systems and the occurrence of such reactions can inflict permanent damage to the DNA.

Carcinogenicity of acrylamide: a computational study

This paper reports a series of ab initio, density functional theory (DFT), and semiempirical molecular orbital (MO) calculations concerning the reaction between the ultimate carcinogen of acrylamide and guanine. Acrylamide--a product of the Maillard reaction--is present in a variety of fried and oven-cooked food. After intake, it is epoxidized by cytochrome P450 2E1 to yield the ultimate carcinogen--glycidamide. Effects of solvation were considered using the Langevin dipoles (LD) model of Florian and Warshel and the solvent reaction field (SCRF) model of Tomasi and co-workers. In silico activation free energies are in very good agreement with the experimental value of 22.8 kcal/mol. This agreement presents strong evidence in favor of the validity of the proposed S N2 reaction mechanism and points to the applicability of quantum chemical methods to studies of reactions associated with carcinogenesis. In addition, insignificant stereoselectivity of the studied reaction was predicted. Finally, the competing reaction of glycidamide with adenine was simulated, and the experimentally observed regioselectivity was successfully reproduced.