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Natural Product Neopeltolide as a Cytochrome bc₁ Complex Inhibitor: Mechanism of Action and Structural Modification

Zhu, Xiao-Lei, Zhang, Rui, Wu, Qiong-You, Song, Yong-Jun, Wang, Yu-Xia, Yang, Jing-Fang, Yang, Guang-Fu
Journal of agricultural and food chemistry 2019 v.67 no.10 pp. 2774-2781
NADH dehydrogenase, chemical structure, computer simulation, diphenyl ethers, fungicides, hydrogen bonding, inhibitory concentration 50, mechanics, mechanism of action, mitochondria, molecular dynamics, molecular models, simulation models, surface area, swine
The marine natural product neopeltolide was isolated from a deep-water sponge specimen of the family Neopeltidae. Neopeltolide has been proven to be a new type of inhibitor of the cytochrome bc₁ complex in the mitochondrial respiration chain. However, its detailed inhibition mechanism has remained unknown. In addition, neopeltolide is difficult to synthesize because of its very complex chemical structure. In the present work, the binding mode of neopeltolide was determined for the first time by integrating molecular docking, molecular dynamics simulations, and molecular mechanics Poisson–Boltzmann surface area calculations, which showed that neopeltolide is a Qₒ site inhibitor of the bc₁ complex. Then, according to guidance via inhibitor–protein interaction analysis, structural modification was carried out with the aim to simplify the chemical structure of neopeltolide, leading to the synthesis of a series of new neopeltolide derivatives with much simpler chemical structures. The calculated binding energies (ΔGcₐₗ) of the newly synthesized analogues correlated very well (R² = 0.90) with their experimental binding free energies (ΔGₑₓₚ), which confirmed that the computational protocol was reliable. Compound 45, bearing a diphenyl ether fragment, was successfully designed and synthesized as the most potent candidate (IC₅₀ = 12 nM) against porcine succinate cytochrome c reductase. The molecular modeling results indicate that compound 45 formed a π–π interaction with Phe274 and two hydrogen bonds with Glu271 and His161. The present work provides a new starting point for future fungicide discovery to overcome the resistance that the existing bc₁ complex inhibitors are facing.