Modeling Mechanisms of Unusual Benzene Imine N6 Adduct Formation in Carcinogenic Reactions of Arylnitrenium Ions with Adenosine

INSIGHT INTO MECHANISM OF FORMATION OF C8 ADDUCTS IN CARCINOGENIC REACTIONS OF ARYLNITRENIUM IONS WITH PURINE NUCLEOSIDES II: AB INITIO, DFT, AND ABEEM/MM-MD SIMULATION STUDIES OF CHEMICAL REACTIONS CONCERNING N9-SUBSTITUTED PURINE BASES WITH 4-BIPHENYLYLNITRENIUM ION

Theoretical insight into the mechanism of C8 adducts formation in a series of complicated carcinogenic reactions has been provided in a previous work. However, two important issues involved in this mechanism still need to be elucidated in detail. Hence, in this paper, we first present a new theoretical model to study the direct formation mechanism of C8 adduct. It is found that this model can well reflect the actual interactions in the real carcinogenic reactions. Thus, a better theoretical model to simulate other properties of these complicated reactions is found using ab initio and density functional theory (DFT) methods. Second, we simulate the formation process of C8 adduct in this new theoretical model using ABEEM/MM-MD method. According to the MD study, we approve that the higher aqueous-phase activation energy for transition state in this kind of reaction contributes to weaker interactions between central sites of reaction and water compared with those for reactants. This study once more supports the mechanism of formation of C8 adducts in the actual carcinogenic reactions where arylnitrenium ions directly attack at C8 positions of nucleoside bases in DNA.

Conformational flexibility of C8-phenoxylguanine adducts in deoxydinucleoside monophosphates

M06-2X/6-31G(d,p) is used to calculate the structure of all natural deoxydinucleoside monophosphates with G in the 5' or 3' position, the anti or syn conformation, and each natural (A, C, G, T) base in the corresponding flanking position. When the ortho or para C8-phenoxyl-2'-deoxyguanosine (C8-phenoxyl-dG) adduct replaces G in each model, there is little change in the relative base-base orientation or backbone conformation. However, the orientation of the C8-phenoxyl group can be characterized according to the position (5' versus 3'), conformation (anti versus syn), and isomer (ortho versus para) of damage. Although the degree of coplanarity between the phenoxyl ring and G base in the ortho adduct is highly affected by the sequence since the hydroxyl group can interact with neighboring bases, the para adduct generally does not exhibit discrete interactions with flanking bases. For both adducts, steric clashes between the phenoxyl group and the backbone or flanking base destabilize the anti conformation preferred by the natural nucleotide and thereby result in a clear preference for the syn conformation regardless of the sequence or position. This contrasts the conclusions drawn from smaller (nucleoside, nucleotide) models previously used in the literature, which stresses the importance of using models that address the steric constraints present due to the surrounding environment. Since replication errors for other C8-dG bulky adducts have been linked to a preference for the syn conformation, our findings provide insight into the possible mutagenicity of phenolic adducts.

Insight into mechanism of formation of c8 adducts in carcinogenic reactions of arylnitrenium ions with purine nucleosides

For the most important arylnitrenium ion-guanosine C8 adducts in the reactions involving arylamine-initiated carcinogenesis, a detailed mechanism of their formation still remains unclear. In this paper, we employ quantum chemistry methods to explore this issue. Our study indicates that formation of these C8 adducts proceeds directly by additions of arylnitrenium ions to C8 position of nucleoside bases in DNA. The good agreements of theoretical rate constants, pK(a) value, and NMR chemical shifts of C8 intermediate with experimental data support this theoretical finding. Excitingly, predictions of what adducts can be observed in reactions of arylnitrenium ions with guanine and hypoxanthine are in fair agreement with experimental observations. This study answers an important question, in carcinogenesis researches, of what is the mechanism for formation of C8 adducts.