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Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors

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Abstract

Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists to predict the binding affinity accurately without detailed structural information for protein / ligand complex. We investigated the absolute binding free energies for Poly (ADP-ribose) polymerase-1 (PARP-1) / inhibitor complexes, using the MP-CAFEE method. Although each docking model was used as an input structure, it was found that the absolute binding free energies calculated by MP-CAFEE are well consistent with the experimental ones. The accuracy of this method is much higher than that using molecular mechanics Poisson-Boltzmann / surface area (MM / PBSA). Although the simulation time is quite extensive, the reliable predictor of binding free energies would be a useful tool for drug discovery projects.

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Acknowledgments

The authors thank E. Lindahl for help in modifying GROMACS. The authors thank Ms. Mariko Katsuyama, Mr. Makoto Takeuchi, Dr. Yuzo Matsumoto, Ms. Naoko Katayama, Dr. Makoto Oku, Ms. Ayako Moritomo, Dr. Kenichi Mori, and Dr. Hideyoshi Fuji for helpful discussions.

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Authors and Affiliations

  1. Drug Discovery Research, Astellas Pharma Inc., 21 Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan

    Kazuki Ohno, Tatsuya Niimi & Masaya Orita

  2. Fujitsu Ltd., 1-9-3 Nakase, Mihama, Chiba, 261-8588, Japan

    Takashi Mitsui

  3. Fujitsu Laboratories Ltd., 10-1 Morinosato-Wakamiya, Atsugi, 243-0197, Japan

    Yoshiaki Tanida, Azuma Matsuura & Hideaki Fujitani

Authors
  1. Kazuki Ohno
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  2. Takashi Mitsui
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  3. Yoshiaki Tanida
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  4. Azuma Matsuura
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  5. Hideaki Fujitani
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  6. Tatsuya Niimi
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  7. Masaya Orita
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Corresponding author

Correspondence to Masaya Orita.

Additional information

Kazuki Ohno and Takashi Mitsui equally contribute to this work.

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Ohno, K., Mitsui, T., Tanida, Y. et al. Docking study and binding free energy calculation of poly (ADP-ribose) polymerase inhibitors. J Mol Model 17, 383–389 (2011). https://doi.org/10.1007/s00894-010-0728-2

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  • DOI: https://doi.org/10.1007/s00894-010-0728-2

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