Understanding the mechanism of drug resistance due to a codon deletion in protoporphyrinogen oxidase through computational modeling.
Protoporphyrinogen oxidase (PPO; EC 1.3.3.4) is the last common enzyme for the enzymatic transformation of protoporphyrinogen-IX to protoporphyrin-IX, which is the key common intermediate leading to heme and chlorophyll. Hence, PPO has been identified as one of the most importance action targets for the treatment of some important diseases including cancer and variegated porphyria (VP). In the agricultural field, PPO inhibitors have been used as herbicides for many years. Recently, a unique drug resistance was found to be associated with a nonactive site residue (Gly210) deletion rather than substitution in A. tuberculatus PPO. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) calculations, have been carried out to uncover the detailed molecular mechanism of drug resistance associated with Gly210 deletion. Although Gly210 in the wild-type A. tuberculatus PPO has no direct interaction with the inhibitors, all the computational models and energetic results indicated that Gly210 deletion has great effects on the hydrogen-bonding network and the conformational change of the binding pocket. An interchain hydrogen bond between Gly210 with Ser424, playing an important role in stabilizing the local conformation of the wild-type enzyme, disappeared after Gly210 deletion. As a result, the mutant-type PPO has a lower affinity than the wild-type enzyme, which accounts for the molecular mechanism of drug resistance. The structural and mechanistic insights obtained from the present study provide a new starting point for future rational design of novel PPO inhibitors to overcome drug resistance associated with Gly210 deletion.
Hao
Ge-Fei
GF
Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, PR China.
Zhu
Xiao-Lei
XL
Ji
Feng-Qin
FQ
Zhang
Li
L
Yang
Guang-Fu
GF
Zhan
Chang-Guo
CG
D027721:Amaranthus / Q000201:enzymology; D003062:Codon / Q000235:genetics*; D003198:Computer Simulation; D004351:Drug Resistance; D004791:Enzyme Inhibitors / Q000737:chemistry / Q000494:pharmacology; D017353:Gene Deletion; D006860:Hydrogen Bonding; D008024:Ligands; D008956:Models, Chemical; D015394:Molecular Structure; D050768:Protoporphyrinogen Oxidase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics*; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D003062:Codon; D004791:Enzyme Inhibitors; D008024:Ligands; D050768:Protoporphyrinogen Oxidase