Skip to main content
SpringerLink
Log in

Exploration of the binding properties of the human serum albumin sites with neurology drugs by docking and molecular dynamics simulation

  • Original Paper
  • Published:
Journal of the Iranian Chemical Society Aims and scope Submit manuscript

Abstract

In this study, the binding properties of a set of neurology drugs to human serum albumin (HSA) were studied by docking and molecular dynamic (MD) methods. Based on the RMSD values for the MD simulation processes, the drug–protein complexes are stable. Site II of the HSA shows the best affinity for the studied drugs. Different kinds of interactions, including hydrogen bonding, π-cation interactions, and π–π interactions, are observable between ligand and protein during the MD simulation process. The MMGBSA calculations were done to evaluate the binding energy of the ligands and protein. The calculated energies are in good agreement with the previously reported experimental results. In some cases, there is a direct relation between the calculated binding energy with the half-life of the drugs, as it was expected.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Abbreviations

HSA:

Human serum albumin

TI:

Thermodynamic integration

FEP:

Free energy perturbation

LIE:

Linear interaction energy

MM/GB–SA:

Molecular mechanics/generalized born and surface area

MM/PB–SA:

Molecular mechanics/Poisson–Boltzmann and surface area

MD:

Molecular dynamic

PME:

Particle mesh Ewald

LJ:

Lennard-Jones

RMSD:

Root-mean-square deviation

TIP3P:

Transferable intermolecular potential 3 point

MC:

Monte Carlo

LGA:

Lamarckian genetic algorithm

References

  1. C.B. Anfinsen, J.T. Edsall, F.M. Richards, D.S. Eisenberg (eds.), Advances in Protein Chemistry (Academic Press, New York, 1994)

    Google Scholar 

  2. O. Deeb, M.C. Rosales-Hernández, C. Gómez-Castro, R. Garduño-Juárez, J. Correa-Basurto, Biopolymers 93, 161 (2010)

    Article  CAS  Google Scholar 

  3. T. Peters Jr., All about albumin: biochemistry, genetics, and medical applications (Academic press, California, 1995)

    Google Scholar 

  4. Y. Li, W. He, H. Liu, X. Yao, Z. Hu, J. Mol. Struct. 831, 144 (2007)

    Article  CAS  Google Scholar 

  5. P.L.V. Falé, L. Ascensão, M.L.M. Serralheiro, P.I. Haris, Spectrosc. Int. J. 26, 79 (2011)

    Article  Google Scholar 

  6. A. Varshney, P. Sen, E. Ahmad, M. Rehan, N. Subbarao, R.H. Khan, Chirality 22, 77 (2010)

    Article  CAS  Google Scholar 

  7. H. Dezhampanah, A.K. Bordbar, S. Farshad, Spectroscopy 25, 235 (2011)

    Article  CAS  Google Scholar 

  8. U. Kragh-Hansen, V.T.G. Chuang, M. Otagiri, Biol. Pharm. Bull. 25, 695 (2002)

    Article  CAS  Google Scholar 

  9. X.M. He, D.C. Carter, Nature 358, 209 (1992)

    Article  CAS  Google Scholar 

  10. N. Ota, D.A. Agard, J. Mol. Biol. 314, 607 (2001)

    Article  CAS  Google Scholar 

  11. J. Ghuman, P.A. Zunszain, I. Petitpas, A.A. Bhattacharya, M. Otagiri, S. Curry, J. Mol. Biol. 353, 38 (2005)

    Article  CAS  Google Scholar 

  12. R. Brodersen, T. Sjödin, I. Sjöholm, J. Biol. Chem. 252, 5067 (1977)

    CAS  Google Scholar 

  13. A. Sułkowska, J. Mol. Struct. 614, 227 (2002)

    Article  Google Scholar 

  14. O. Noriaki, F. Noriyuki, F. Hideyoshi, S. Atsushi, M. Gentaro, Y. Ryoko, O. Yousuke, N. Tetsu, T. Makoto, PLOS Comput. Biol. 5(10), e1000528 (2009)

    Article  Google Scholar 

  15. D.A. Pearlman, P.S. Charifson, J. Med. Chem. 44, 3417 (2001)

    Article  CAS  Google Scholar 

  16. P. Kollman, Chem. Rev. 93, 2395 (1993)

    Article  CAS  Google Scholar 

  17. J. Åqvist, V.B. Luzhkov, B.O. Brandsdal, Acc. Chem. Res. 35, 358 (2002)

    Article  Google Scholar 

  18. P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, T.E. Cheatham, Acc. Chem. Res. 33, 889 (2000)

    Article  CAS  Google Scholar 

  19. S. Huo, J. Wang, P. Cieplak, P.A. Kollman, I.D. Kuntz, J. Med. Chem. 45, 1412 (2002)

    Article  CAS  Google Scholar 

  20. B. Kuhn, P. Gerber, T. Schulz-Gasch, M. Stahl, J. Med. Chem. 48, 4040 (2005)

    Article  CAS  Google Scholar 

  21. M. Hanwell, D. Curtis, D. Lonie, T. Vandermeersch, E. Zurek, G. Hutchison, J. Cheminform. 4, 17 (2012)

    Article  CAS  Google Scholar 

  22. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery Jr., J. E. Peralta, F. Ogliaro, M. J. Bearpark, J. Heyd, E. N. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. P. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, N. J. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J. B. Foresman, J. V. Ortiz, J. Cioslowski, D. J. Fox (Gaussian, Inc., Wallingford, CT, USA, 2009)

  23. G.M. Morris, D.S. Goodsell, R.S. Halliday, R. Huey, W.E. Hart, R.K. Belew, A.J. Olson, J. Comput. Chem. 19, 1639 (1998)

    Article  CAS  Google Scholar 

  24. J. Gasteiger, M. Marsili, Tetrahedron 36, 3219 (1980)

    Article  CAS  Google Scholar 

  25. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.J. Olson, J. Comput. Chem. 30, 2785 (2009)

    Article  CAS  Google Scholar 

  26. H.J.C. Berendsen, D. van der Spoel, R. van Drunen, Comput. Phys. Commun. 91, 43 (1995)

    Article  CAS  Google Scholar 

  27. D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, H.J.C. Berendsen, J. Comput. Chem. 26, 1701 (2005)

    Article  Google Scholar 

  28. E. Lindahl, B. Hess, D. van der Spoel, J. Mol. Model. 7, 306 (2001)

    Article  CAS  Google Scholar 

  29. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 98, 10089 (1993)

    Article  CAS  Google Scholar 

  30. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, J. Chem. Phys. 103, 8577 (1995)

    Article  CAS  Google Scholar 

  31. J. Wang, W. Wang, P.A. Kollman, D.A. Case, J. Mol. Graph. Model. 25, 247 (2006)

    Article  Google Scholar 

  32. D. Case, P. Kollaman, AmberTools 12 (University of California, San Francisco, 2012)

  33. A.W. Sousa da Silva, W.F. Vranken, BMC Res. Notes 5, 367 (2012)

    Article  Google Scholar 

  34. W.C. Swope, H.C. Andersen, P.H. Berens, K.R. Wilson, J. Chem. Phys. 76, 637 (1982)

    Article  CAS  Google Scholar 

  35. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, M.L. Klein, J. Chem. Phys. 79, 926 (1983)

    Article  CAS  Google Scholar 

  36. H.J.C. Berendsen, J.P.M. Postma, W.F. Van Gunsteren, A. Dinola, J.R. Haak, J. Chem. Phys. 81, 3684 (1984)

    Article  CAS  Google Scholar 

  37. M. Parrinello, A. Rahman, J. Appl. Phys. 52, 7182 (1981)

    Article  CAS  Google Scholar 

  38. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, T.E. Ferrin, J. Comput. Chem. 25, 1605 (2004)

    Article  CAS  Google Scholar 

  39. W. Humphrey, A. Dalke, K. Schulten, J. Mol. Graph. 14, 33 (1996)

    Article  CAS  Google Scholar 

  40. Studio, D. 3.5 (Accelrys Software Inc., San Diego, CA, 2012)

  41. T. Hou, J. Wang, Y. Li, W. Wang, J. Chem. Inf. Model. 51, 69 (2011)

    Article  CAS  Google Scholar 

  42. L.H.M. Janssen, J.H.M. Dröge, F.J. Durlinger, Thermochim. Acta 172, 197 (1990)

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We gratefully acknowledge the financial support of the research council of Shahid Beheshti University. Also, the technical support of the computational chemistry center at Shahid Beheshti University is gratefully acknowledged.

Author information

Authors and Affiliations

  1. Faculty of Chemistry, Shahid Beheshti University, G.C., Evin, Tehran, 19839-63113, Iran

    Fatemeh S. Alavi & Mansour Zahedi

  2. Computational Chemistry Laboratory, Department of Organic and Biochemistry, Faculty of Chemistry, University of Tabriz, Tabriz, 5166616471, Iran

    Rahim Ghadari

Authors
  1. Fatemeh S. Alavi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rahim Ghadari
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mansour Zahedi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mansour Zahedi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 694 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Alavi, F.S., Ghadari, R. & Zahedi, M. Exploration of the binding properties of the human serum albumin sites with neurology drugs by docking and molecular dynamics simulation. J IRAN CHEM SOC 14, 19–35 (2017). https://doi.org/10.1007/s13738-016-0954-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13738-016-0954-3

Keywords

Search

Navigation