Computational Exploration of Dibenzo [a,l] Pyrene Interaction to DNA and its Bases: Possible Implications to Human Health

Dibenzo[a,l]pyrene (DBP), an environmental pollutant, undergoes a series of enzymatic reactions yielding electrophilic diastereomeric diol-epoxides (DEs) that subsequently bind to DNA covalently and hampers the healing mechanism of cascaded biological pathways resulting in onset of different diseases. In the proposed work, we meticulously investigated and elucidated the mechanistic details of DNA adduct formation and nucleotide excision repair (NER) pathway proteins interaction with all possible diastereomers of dibenzo[a,l]pyrene-diol-epoxides (DBPDEs) namely- (±)-anti-, (±)-syn-, trans- and cis- forms of (-)-anti- and (+)-syn- DBPDEs through a computational simulation study. Our findings revealed that (±)-anti- and (-)-syn-DBPDEs interact more strongly with dT20 while (+)-syn-DBPDE exhibits strong interaction with dG6. Moreover, cis- and trans-conformations of (-)-anti- and (+)-syn-DBPDEs depicted strong binding towards N6-dA. Furthermore, aforesaid metabolic intermediates exhibited weak interactions with NER proteins. This imbalance of interaction tendencies relatively favors the DNA-adduct formation than the NER pathway. Based on our computational data, a robust understanding of the underlying molecular mechanism(s) of DBP-DNA interactions may subsequently lead to the design of novel potential compounds to exert inhibition and block its DNA binding ability and eventually facilitate cancer prevention.

Epoxide formation from heterogeneous oxidation of benzo[a]pyrene with gas-phase ozone and indoor air

This work demonstrates the production of mono- and diol-epoxides from heterogeneous oxidation of benzo[a]pyrene with gas-phase ozone.

Structural basis for error-free bypass of bulky adduct by DNA polymerase Polκ

Humans are frequently exposed to the environmentally ubiquitous and potentially carcinigenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). BP is metabolized to highly reactive benzo[a]pyrene diol epoxides (BPDEs) in the cells. BPDEs react with DNA predominantly at the N2 position of guanine and form bulky adducts. The major BP adduct is (+)-trans-anti-[BP]-N2-dG (BP-N2-dG) that is carcinogenic. The bulky adduct block DNA synthesis by replicative or high-fidelity DNA polymerases. Some of the specialized lesion bypass polymerases (mostly belonging to Y-family) can replicate through this bulky adduct but often in an error prone manner, resulting in mutagenesis. Among the four human Y-family polymerases Polη, Polκ, Polι and Rev1, Polκ is unique in its ability for efficient and error-free replication through BP induced BP-N2-dG adduct. In this study, we determined the crystal structures of human Polκ (hPolκ) in ternary complex with DNA and an incoming nucleotide dCTP analogue. The crystals contain DNA with either G base or (+)-trans-anti-[BP]-N2-dG adduct at a template-primer junction and diffract to 2.5 Å and 2.8 Å, respectively. The structures reveal that hPolκ is able to accommodate the bulky adducted DNA in its minor groove without base flipping and nucleotide looping out. The bulky adduct has the polycyclic BP moiety in the minor groove in the regular helical conformation. Polκ has a unique active site that is more open at the minor groove side than other Y-family polymerases. The damaged guanine is in the anti-conformation, the dCMPNPP incoming nucleotide maintains normal Watson-Crick pairing with the G* base. This is the first structure of eukaryotic Y-family polymerase carrying the minor groove BP adduct. The structure and biochemical analysis provides a basis for understanding how hPolκ can correctly bypass and tolerate BP induced BP-N2-dG adduct in human cells.