Effects of water models on binding affinity: Evidence from all-atom simulation of binding of tamiflu to A/H5N1 neuraminidase

The Scientific World Journal

Volumn 2014, Issue , 2014, Pages

  Nguyen, Trang Truc ^a   Viet, Man Hoang ^b   Li, Mai Suan ^b  

^a INSTITUTE FOR COMPUTATIONAL SCIENCE AND TECHNOLOGY   (Viet Nam)

^b INSTITUTE OF PHYSICS   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

4 ACETAMIDO 5 AMINO 3 (1 ETHYLPROPOXY) 1 CYCLOHEXENE 1 CARBOXYLIC ACID; OSELTAMIVIR; SIALIDASE; WATER; ANTIVIRUS AGENT;

ARTICLE; ATOM; BINDING AFFINITY; CONTROLLED STUDY; DENSITY; DRUG BINDING; ENERGY; ENZYME BINDING; FORCE; INFLUENZA VIRUS A H5N1; LIGAND BINDING; MOLECULAR MODEL; NONHUMAN; SCORING SYSTEM; SIMULATION; WILD TYPE; CHEMISTRY; ENZYMOLOGY; METABOLISM; POISSON DISTRIBUTION;

ANTIVIRAL AGENTS; INFLUENZA A VIRUS, H5N1 SUBTYPE; NEURAMINIDASE; OSELTAMIVIR; POISSON DISTRIBUTION; WATER;

EID: 84896864699     PISSN: None     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1155/2014/536084     Document Type: Article

References (48)

1. Kollman P. A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., Donini O., Cieplak P., Srinivasan J., Case D. A., Cheatham T. E. III, Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Accounts of Chemical Research 2000 33 12 889 897 2-s2.0-0034521981 10.1021/ar000033j
2. Kirkwood J. G., Statistical mechanics of fluid mixtures. The Journal of Chemical Physics 1935 3 5 300 313 2-s2.0-33646471468
3. Aqvist J., Medina C., Samuelsson J.-E., A new method for predicting binding affinity in computer-aided drug design. Protein Engineering 1994 7 3 385 391 2-s2.0-0028155689
4. Zwanzig R. W., High-temperature equation of state by a perturbation method. I. Nonpolar gases. The Journal of Chemical Physics 1954 22 12 1420 1426 10.1063/1.1740409
5. Karplus M., McCammon J. A., Molecular dynamics simulations of biomolecules. Nature Structural Biology 2002 9 9 646 652 2-s2.0-0036725277 10.1038/nsb0902-646
6. Lee F. S., Chu Z.-T., Bolger M. B., Warshel A., Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Protein Engineering 1992 5 3 215 228 2-s2.0-0026596911
7. Bren U., Lah J., Bren M., Martnek V., Florin J., DNA duplex stability: the role of preorganized electrostatics. Journal of Physical Chemistry B 2010 114 8 2876 2885 10.1021/jp9064246
8. Grubmüller H., Heymann B., Tavan P., Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 1996 271 5251 997 999 2-s2.0-0030059225
9. Mai B. K., Viet M. H., Li J M. S., Top leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach. Journal of Chemical Information and Modeling 2010 50 12 2236 2247 10.1021/ci100346s
10. Berendsen J. H. C., Postma J. P. M., van Gunsteren W. F., Hermans J., Pullmann B., Interaction models for water in relation to protein hydration. Intermolecular Forces 1981 331 342
11. Berendsen H. J. C., Grigera J. R., Straatsma T. P., The missing term in effective pair potentials. Journal of Physical Chemistry 1987 91 24 6269 6271 2-s2.0-1242346370
12. Jorgensen W. L., Chandrasekhar J., Madura J. D., Impey R. W., Klein M. L., Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics 1983 79 2 926 935 2-s2.0-0004016501
13. Jorgensen W. L., Madura J. D., Temperature and size dependence for Monte Carlo simulations of TIP4P water. Molecular Physics 1985 56 6 1381 1392 10.1080/00268978500103111
14. Hess B., van der Vegt N. F. A., Hydration thermodynamic properties of amino acid analogues: a systematic comparison of biomolecular force fields and water models. Journal of Physical Chemistry B 2006 110 35 17616 17626 2-s2.0-33748791718 10.1021/jp0641029
15. Florova P., Sklenovsky P., Banas P., Otyepka M., Explicit water models affect the specific solvation and dynamics of unfolded peptides while the conformational behavior and flexibility of folded peptides remain intact. Journal of Chemical Theory and Computation 2010 6 11 3569 3579 10.1021/ct1003687
16. Hu Z., Jiang J., Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal. Journal of Computational Chemistry 2009 31 2 371 380 10.1002/jcc.21330
17. Almlof M., Brandsdal B. O., Aqvist J., Binding affinity prediction with different force fields: examination of the linear interaction energy method. Journal of Computational Chemistry 2004 25 10 1242 1254 10.1002/jcc.20047
18. Nguyen T. T., Mai B. K., Li M. S., Study of tamiflu sensitivity to variants of A/H5N1 virus using different force fields. Journal of Chemical Information and Modeling 2011 51 9 2266 2276 2-s2.0-80053300058 10.1021/ci2000743
19. Cozzini P., Fornabaio M., Marabotti A., Abraham D. J., Kellogs G. E., Mozzarelli A., Free energy of ligand binding to protein: evaluation of the contribution of water molecules by computational methods. Current Medicinal Chemistry 2004 11 23 3093 3118 2-s2.0-4143121554
20. Michel J., Tirado-Rives J., Jorgensen W. L., Prediction of the water content in protein binding sites. Journal of Physical Chemistry B 2009 113 40 13337 13346 2-s2.0-70349683018 10.1021/jp9047456
21. Wang L., Berne B. J., Friesner R. A., Ligand binding to protein-binding pockets with wet and dry regions. Proceedings of the National Academy of Sciences of the United States of America 2011 108 4 1326 1330 10.1073/pnas.1016793108
22. Chaplin M., Water structure and science. 2000, http://www.lsbu.ac.uk/ water/
23. Collins P. J., Haire L. F., Lin Y. P., Liu J., Russell R. J., Walker P. A., Skehel J. J., Martin S. R., Hay A. J., Gamblin S. J., Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature 2008 453 7199 1258 1261 2-s2.0-46249111790 10.1038/nature06956
24. Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C., Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 2006 65 3 712 725 2-s2.0-33748518255 10.1002/prot.21123
25. Brooks B. R., Brooks C. L., Mackerell A. D., CHARMM: the biomolecular simulation program. Journal of Computational Chemistry 2009 30 10 1545 1614 10.1002/jcc.21287
26. Jorgensen W. L., Tirado-Rives J., The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society 1988 110 6 1657 1666 2-s2.0-33645941402
27. van Gunsteren W. F., Billeter S. R., Eising A. A., Hunenberger P. H., Kruger P., Mark A. E., Scott W. R. P., Tironi I. G., Biomolecular Simulation: The GROMOS96 Manual and User Guide 1996 Zurich, Switzerland Vdf Hochschulverlag AG an der ETH Zurich
28. Webster R. G., Govorkova E. A., H5N1 influenza-continuing evolution and spread. The New England Journal of Medicine 2006 355 21 2174 2177 2-s2.0-33751231111 10.1056/NEJMp068205
29. The Writing Committee of the World Health Organization (WHO) Consultation on Human Influenza A/H5, Avian influenza A (H5N1) infection in humans. The New England Journal of Medicine 2005 353 13 1374 1385 10.1056/NEJMra052211
30. Schrödinger, PyMOL: The PyMOL Molecular Graphics System, Version 1.3 2010 Schrödinger
31. van Aalten D. M. F., Bywater R., Findlay J. B. C., Hendlich M., Hooft R. W. W., Vriend G., PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. Journal of Computer-Aided Molecular Design 1996 10 3 255 262 10.1007/BF00355047
32. Frisch M. J., Trucks G. W., Schlegel H. B., Gaussian 03, Revision C.02 2004 Wallingford, Conn, USA Gaussian
33. Silva A. W. S. D., Vranken W. F., Laue E. D., ACPYPE-AnteChamber PYthon Parser interfacE. submitted
34. Andre A. S. T. R., Bruno A. C. H., Ricardo B. A., MKTOP: a program for automatic construction of molecular topologies. Journal of the Brazilian Chemical Society 2008 19 7 1433 1435 10.1590/S0103-50532008000700031
35. Zoete V., Cuendet M. A., Grosdidier A., Michielin O., SwissParam: a fast force field generation tool for small organic molecules. Journal of Computational Chemistry 2011 32 11 2359 2368 2-s2.0-79958841703 10.1002/jcc.21816
36. Guillot B., A reappraisal of what we have learnt during three decades of computer simulations on water. Journal of Molecular Liquids 2002 101 1-3 219 260 10.1016/S0167-7322(02)00094-6
37. Bernal J. D., Fowler R. H., A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. The Journal of Chemical Physics 1933 1 8 515 548 2-s2.0-0346735076
38. Darden T., York D., Pedersen L., Particle mesh Ewald: an N · log(N) method for Ewald sums in large systems. The Journal of Chemical Physics 1993 98 12 10089 10092 2-s2.0-33846823909
39. Hockney R. W., Goel S. P., Eastwood J. W., Quiet high-resolution computer models of a plasma. Journal of Computational Physics 1974 14 2 148 158 2-s2.0-0347784245
40. Berendsen H. J. C., Postma J. P. M., van Gunsteren W. F., Dinola A., Haak J. R., Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics 1984 81 8 3684 3690 2-s2.0-33750587438
41. Parrinello M., Rahman A., Polymorphic transitions in single crystals: a new molecular dynamics method. Journal of Applied Physics 1981 52 12 7182 7190 2-s2.0-0019707626 10.1063/1.328693
42. Hess B., Kutzner C., van der Spoel D., Lindahl E., GRGMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 2008 4 3 435 447 2-s2.0-46249092554 10.1021/ct700301q
43. Cheng L. S., Amaro R. E., Xu D., Li W. W., Arzberger P. W., McCammon J. A., Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. Journal of Medicinal Chemistry 2008 51 13 3878 3894 2-s2.0-46849105028 10.1021/jm8001197
44. Barber C. B., Dobkin D. P., Huhdanpaa H., The quickhull algorithm for convex hulls. ACM Transactions on Mathematical Software 1996 22 4 469 483 2-s2.0-0030381077
45. Clarkson K. L., Menlhorn K., Seidel R., Four results on randomized incremental constructions. Computational Geometry 1993 3 4 185 212 10.1016/0925-7721(93)90009-U
46. Chau P. L., Water movement during Ligand Unbinding from receptor site. Biophysical Journal 2004 87 1 121 128 10.1529/biophysj.103.036467
47. MATLAB Version 7.0.1 (R2007a) 2007 Natick, Mass, USA The MathWorks Inc.
48. Aruksakunwong O., Malaisree M., Decha P., Sompornpisut P., Parasuk V., Pianwanit S., Hannongbua S., On the lower susceptibility of oseltamivir to influenza neuraminidase subtype N1 than those in N2 and N9. Biophysical Journal 2007 92 3 798 807 2-s2.0-33846839226 10.1529/biophysj.106.092528