Molecular docking simulation of anaerobic biodegradation pathways of petroleum hydrocarbons in oil reservoir

In-depth study of the anaerobic biodegradation mechanism of petroleum hydrocarbons is of great significance for microbial oil recovery and bioremediation. This study retrieved microorganisms with genes for anaerobic hydrocarbon degradation from the PATRIC and NCBI databases, and compiled taxonomic information of core microorganisms containing multiple functional genes. Molecular docking simulations were conducted on 11 enzymes involved in the initial degradation pathways, such as fumarate addition reaction, anaerobic hydroxylation, and anaerobic carboxylation. The simulations revealed the petroleum hydrocarbon binding energy, binding affinity, and binding site within the enzyme cavity. The results indicated that the core microbial bacterial lineages with anaerobic degradation functional genes mainly included Bacillota and Proteobacteria. Enzymes in the same initial degradation pathway continuously catalysed the anaerobic degradation of petroleum hydrocarbons through synergistic action. The interaction force between catalytic enzymes and petroleum hydrocarbons was mainly hydrophobic interaction, with some π-π stacking interaction. This study conducted the first molecular simulation of anaerobic degradation of petroleum hydrocarbons, illustrating the interaction mode between petroleum hydrocarbons and enzymes, as well as the anaerobic degradation mechanism of petroleum hydrocarbons. •Microorganisms with multiple anaerobic degradation functional genes are mainly found in Proteobacteria and Firmicutes.•The main force between degrading enzymes and alkanes is hydrophobic interaction, with π-π stacking for arenes.•Arnes, due to their benzene ring, don’t follow the rule that lower binding energy increases biodegradation rates.