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Probing possible egress channels for multiple ligands in human CYP3A4: A molecular modeling study

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Abstract

Human cytochrome P450 (CYP) 3A4 extensively contributes to metabolize 50% of the marketed drugs. Recently, a CYP3A4 structure with two molecules of ketoconazole (2KT) was identified. However, channels for egresses of these inhibitors are unexplored. Thus, we applied molecular dynamics simulations followed by channel analyses. Two simulations of empty and 2KT-bound CYP3A4 results revealed the multiple ligand-induced conformational changes in channel forming regions, which appear to be important for the regulation of channels. In addition, we observed that the channel-3 entrance is closed due to the large structural deviation of the key residues from Phe-cluster. F215 and F220 are known as entrance blockers of channel-2 in metyrapone-bound CYP3A4. Currently, F220 blocks the channel-3 along with F213 and F241. Therefore, it suggested that channel-1 and 2 could potentially serve as egress routes for 2KT. It is also supported by the results from MOLAxis analyses, in which the frequency of channel occurrence and bottleneck radius during simulation favor channel-1 and 2. Several bottleneck residues of these channels may have critical roles in 2KT egresses, especially S119. Our modeling study for multiple ligand-channeling of CYP3A4 could be very helpful to gain new insights into channel selectivity of CYP3A4.

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Acknowledgments

The authors express their great gratitude to the reviewers for their valuable suggestions. N. Krishnamoorthy, P. Gajendrarao, S. Thangapandian and Y. Lee were supported by scholarship from the BrainKorea21 program, Ministry of Education, Science and Technology, Korea and this work was supported by grants from MOST/KOSEF for Environmental Biotechnology National Core Research Center (grant #:R15–2003–012–02001–0).

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Authors and Affiliations

  1. Department of Biochemistry, Division of Applied Life Science (BK21 program), Environmental Biotechnology National Core Research Center, Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Korea

    Navaneethakrishnan Krishnamoorthy, Poornima Gajendrarao, Sundarapandian Thangapandian, Yuno Lee & Keun Woo Lee

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  1. Navaneethakrishnan Krishnamoorthy
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  2. Poornima Gajendrarao
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  3. Sundarapandian Thangapandian
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  4. Yuno Lee
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  5. Keun Woo Lee
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Corresponding author

Correspondence to Keun Woo Lee.

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Navaneethakrishnan Krishnamoorthy and Poornima Gajendrarao contributed equally to this work.

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Krishnamoorthy, N., Gajendrarao, P., Thangapandian, S. et al. Probing possible egress channels for multiple ligands in human CYP3A4: A molecular modeling study. J Mol Model 16, 607–614 (2010). https://doi.org/10.1007/s00894-009-0571-5

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  • DOI: https://doi.org/10.1007/s00894-009-0571-5

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