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.
Ge-Fei Hao Xiao-Lei Zhu Feng-Qin Ji Li Zhang Guang-Fu Yang Chang-Guo Zhan
Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Centr Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 725 Rose Street,
国际会议
武汉
英文
151-161
2010-09-01（万方平台首次上网日期，不代表论文的发表时间）