title: Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations.
abstract: As a promising target for the treatment of lung cancer, the MutT Homolog 1 (MTH1) protein can be inhibited by crizotinib. A recent work shows that the inhibitory potency of (S)-crizotinib against MTH1 is about 20 times over that of (R)-crizotinib. But the detailed molecular mechanism remains unclear. In this study, molecular dynamics (MD) simulations and free energy calculations were used to elucidate the mechanism about the effect of chirality of crizotinib on the inhibitory activity against MTH1. The binding free energy of (S)-crizotinib predicted by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Adaptive biasing force (ABF) methodologies is much lower than that of (R)-crizotinib, which is consistent with the experimental data. The analysis of the individual energy terms suggests that the van der Waals interactions are important for distinguishing the binding of (S)-crizotinib and (R)-crizotinib. The binding free energy decomposition analysis illustrated that residues Tyr7, Phe27, Phe72 and Trp117 were important for the selective binding of (S)-crizotinib to MTH1. The adaptive biasing force (ABF) method was further employed to elucidate the unbinding process of (S)-crizotinib and (R)-crizotinib from the binding pocket of MTH1. ABF simulation results suggest that the reaction coordinates of the (S)-crizotinib from the binding pocket is different from (R)-crizotinib. The results from our study can reveal the details about the effect of chirality on the inhibition activity of crizotinib to MTH1 and provide valuable information for the design of more potent inhibitors.
authors.affiliation: State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Yuzhen
authors.initials: Y
authors.lastname: Niu
authors.affiliation: State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Dabo
authors.initials: D
authors.lastname: Pan
authors.affiliation: State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Danfeng
authors.initials: D
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Qifeng
authors.initials: Q
authors.lastname: Bai
authors.affiliation: School of Pharmacy, Lanzhou University, Lanzhou, 730000, China.|The Separating Scientific Institute of Lanzhou, Lanzhou, 730000, China.
authors.forename: Huanxiang
authors.initials: H
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, 730000, China.|Key Lab of Preclinical Study for New Drugs of Gansu Province, Lanzhou University, Lanzhou, 730000, China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Yao
mesh_terms: D001665:Binding Sites; D000077547:Crizotinib; D045643:DNA Repair Enzymes / Q000037:antagonists & inhibitors* / Q000378:metabolism; D004734:Energy Metabolism; D006801:Humans; D008962:Models, Theoretical; D056004:Molecular Dynamics Simulation; D010744:Phosphoric Monoester Hydrolases / Q000037:antagonists & inhibitors* / Q000378:metabolism; D011485:Protein Binding; D011720:Pyrazoles / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D011725:Pyridines / Q000737:chemistry / Q000378:metabolism / Q000494:pharmacology*; D013237:Stereoisomerism
chemical_list: D011720:Pyrazoles; D011725:Pyridines; D000077547:Crizotinib; D010744:Phosphoric Monoester Hydrolases; C078207:8-oxodGTPase; D045643:DNA Repair Enzymes