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Exploration of the binding of proton pump inhibitors to human P450 2C9 based on docking and molecular dynamics simulation

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Abstract

Human P450 protein CYP2C9 is one of the major drug-metabolizing isomers, contributing to the oxidation of 16% of the drugs currently in clinical use. To examine the interaction mechanisms between CYP2C9 and proton pump inhibitions (PPIs), we used molecular docking and molecular dynamics (MD) simulation methods to investigate the conformations and interactions around the binding sites of PPIs/CYPP2C9. Results from molecular docking and MD simulations demonstrate that nine PPIs adopt two different conformations (extended and U-bend structures) at the binding sites and position themselves far above the heme of 2C9. The presence of PPIs changes the secondary structures and residue flexibilities of 2C9. Interestingly, at the binding sites of all PPI–CYP2C9 complexes except for Lan/CYP2C9, there are hydrogen-bonding networks made of PPIs, water molecules, and some residues of 2C9. Moreover, there are strong hydrophobic interactions at all binding sites for PPIs/2C9, which indicate that electrostatic interactions and hydrophobic interactions appear to be important for stabilizing the binding sites of most PPIs/2C9. However, in the case of Lan/2C9, the hydrophobic interactions are more important than the electrostatic interactions for stabilizing the binding site. In addition, an interesting conformational conversion from extended to U-bend structures was observed for pantoprazole, which is attributed to an H-bond interaction in the binding pocket, an internal π–π stacking interaction, and an internal electrostatic interaction of pantoprazole.

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Acknowledgments

This work is supported by grants from the National Science Foundation of China (nos. 20236010, 20246002, 20376032, 20706029, and 20876073), Jiangsu Science and Technology Department of China (no. BK2008372), and Nanjing University of Technology of China (no. ZK200803).

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  1. State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemistry and Chemical Engineering, Nanjing University of Technology, Nanjing, 210009, China

    Rongwei Shi, Jinyu Li, Xiaoning Cao, Xiaolei Zhu & Xiaohua Lu

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  1. Rongwei Shi
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  3. Xiaoning Cao
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  4. Xiaolei Zhu
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Correspondence to Xiaolei Zhu or Xiaohua Lu.

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Fig. SI-1

Overall fold of CYP2C9, coloured from blue at the N-terminus to green, to yellow, to red at the C-terminus. The heme group is depicted as a ball mode in the center of the molecule, flanked by helices I and L. The figure was produced using Pymol software (DOC 370 kb)

Fig. SI-2

a–i The binding modes of CYP2C9 docked with lansoprazole (a), pantoprazole (b), rabeprazole (c), omeprazole (d), esomeprazole (e), tenatoprazole (f), leminoprazole (g), ilaprazole (h), and disuprazole (i). Carbon atoms of PPIs and the surrounding residues that are within 4 Å of the PPIs are colored in orange and green, respectively. Dotted black lines represent polar interactions or hydrogen bonds (DOC 1368 kb)

Fig. SI-3

a–g Snapshots of the hydrogen-bonding networks in the binding sites of PPIs/CYP2C9 at 10 ns for Pan/2C9 (a), Ome/2C9 (b), Ten/2C9 (c), Rab/2C9 (d), Lem/2C9 (e), Eso/2C9 (f) and Ila/2C9 (g). Carbon atoms of acid residues and PPIs are colored in green and slate blue, respectively. Each dotted line (black) indicates a hydrogen bond (DOC 1059 kb)

Fig. SI-4

a Two-dimensional schematic representation of hydrogen-bond and hydrophobic interactions. Dashed lines represent hydrogen bonds and spiked residues from hydrophobic interactions with Lan. b Interatomic distances associated with hydrogen-bond interactions of Lan in the binding site of CY2C9 versus MD simulation time. To enhance the visual clarity, the curve of L1 is shifted upward by 0.1 nm. c Center of mass distances associated with hydrophobic interactions of Lan in the binding site of CYP2C9 versus MD simulation time. The curves of D2, D4, D5 and D6 are shifted upward by 0.05, 0.10, 0.40 and 0.45 nm, respectively (DOC 209 kb)

Fig. SI-5

a–d Average RMSFs of free CYP2C9 and PPIs/CYP2C9. a RMSFs for 2C9/Ome (red), 2C9/Lan (green). b RMSFs for 2C9/Lem (deep green), 2C9/Rab (orange) and 2C9/Dis (purple). c RMSFs for 2C9/Eso (deep green) and 2C9/Ila (pink). d RMSFs for 2C9/Pan (dark cyan) and 2C9/Ten (light magenta). For comparison, we have added the RMSF of free CYP2C9 (blue) to a–d. Black lines represent flexible loops and residues (DOC 107 kb)

Fig. SI-6

a–i Interactions of PPIs (lansoprazole, pantoprazole, omeprazole, esomeprazole, rabeprazole, ilaprazole, leminoprazole, tenatoprazole, and disuprazole: a–i, respectively) with CYP2C9. Surface representation of CYP2C9, colored on the basis of electrostatic potentials (−65.207k B T/e to 65.207k B T/e), and PPIs. Surface representation of CYP2C9 shows the PPIs (a–i) bound at the binding site of CYP2C9 (shown as yellow sticks). The dashed lines (black) represent hydrogen bonds (DOC 2432 kb)

Fig. SI-7

a–i Final conformations of the binding sites of PPIs/CYP2C9 after 10 ns of MD simulation for Pan/2C9 (a), Ome/2C9 (b), Ten/2C9 (c), Rab/2C9 (d), Lem/2C9 (e), Eso/2C9 (f), Ila/2C9 (g), Dis/2C9 (h), and Lan/2C9 (i), respectively. Carbon atoms of residues of CYP2C9 and PPIs are colored green and salmon pink, respectively. Each dotted line (black) indicates a hydrogen bond. The residues surrounding the binding sites are represented by secondary structures (DOC 3981 kb)

Fig. Si-8

Snapshots of the binding pocket of 2C9/Pan over time. The surface of the protein is rendered in wheat brown. Pantoprazole and residues are shown as sticks, and their carbon atoms are represented in light brown and green, respectively (DOC 2979 kb)

Table SI-1

Binding energies and docking energies of PPIs/CYP2C9, as obtained from molecular docking (DOC 31 kb)

Table SI-2

The retention times for H-bonds between water molecules and disuprazole or residues in the binding pocket during the MD simulation (DOC 39 kb)

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Shi, R., Li, J., Cao, X. et al. Exploration of the binding of proton pump inhibitors to human P450 2C9 based on docking and molecular dynamics simulation. J Mol Model 17, 1941–1951 (2011). https://doi.org/10.1007/s00894-010-0903-5

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