Towards automated binding affinity prediction using an iterative linear interaction energy approach

International Journal of Molecular Sciences

Volumn 15, Issue 1, 2014, Pages 798-816

  Ruben Vosmeer, C ^a   Pool, René ^a   Van Stee, Mariël F ^a   Perić Hassler, Lovorka ^a   Vermeulen, Nico P E ^a   Geerke, Daan P ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

Author keywords

Aryloxypropanolamines; Automated binding free energy calculation; CYP 2D6; Iterative LIE method

Indexed keywords

CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; LIGAND; PROPANOLAMINE DERIVATIVE; PROTEIN BINDING;

ACCURACY; ARTICLE; BINDING AFFINITY; CLUSTER ANALYSIS; ENERGY; LINEAR INTERACTION ENERGY; MOLECULAR DOCKING; PREDICTION; PROTEIN CONFORMATION; SIMULATION; AUTOMATION; BINDING SITE; CHEMISTRY; METABOLISM; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

AUTOMATION; BINDING SITES; CLUSTER ANALYSIS; CYTOCHROME P-450 CYP2D6; LIGANDS; MOLECULAR DOCKING SIMULATION; PROPANOLAMINES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS;

EID: 84892169834     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms15010798     Document Type: Article

References (38)

1. Chodera, J.D.; Mobley, D.L.; Shirts, M.R.; Dixon, R.W.; Branson, K.; Pande, V.S. Alchemical free energy methods for drug discovery: Progress and challenges. Curr. Opin. Struct. Biol. 2011, 21, 150-160.
2. Parenti, M.D.; Rastelli, G. Advances and applications of binding affinity prediction methods in drug discovery. Biotechnol. Adv. 2012, 30, 244-250.
3. De Graaf, C.; Oostenbrink, C.; Keizers, P.H.J.; van Vugt-Lussenburg, B.M.A.; Commandeur, J.N.M.; Vermeulen, N.P.E. Free energies of binding of R- and S-propranolol to wild-type and F483A mutant cytochrome P450 2D6 from molecular dynamics simulations. Eur. Biophys. J. 2007, 36, 589-599.
4. Stjernschantz, E.; Vermeulen, N.P.E.; Oostenbrink, C. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450. Expert Opin. Drug Metab. Tox. 2008, 4, 513-527.
5. Kirchmair, J.; Williamson, M.J.; Tyzack, J.D.; Tan, L.; Bond, P.J.; Bender, A.; Glen, R.C. Computational prediction of metabolism: Sites, products, SAR, P450 enzyme dynamics, and mechanisms. J. Chem. Inf. Model. 2012, 52, 617-648.
6. Ortiz de Montellano, P. Cytochrome P450: Structure, Mechanism, and Biochemistry, 3rd ed.; Kluwer Academic/Plenum Publishers: New York, NY, USA, 2005.
7. Van Gunsteren, W.F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D.P.; Glaettli, A.; Huenenberger, P.H.; et al. Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. 2006, 45, 4064-4092.
8. Rastelli, G.; Rio, A.D.; Degliesposti, G.; Sgobba, M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J. Comput. Chem. 2010, 31, 797-810.
9. Klebe, G. Virtual ligand screening: Strategies, perspectives and limitations. Drug Discov. Today 2006, 11, 580-594.
10. Christ, C.D.; Mark, A.E.; van Gunsteren, W.F. Basic ingredients of free energy calculations: A review. J. Comput. Chem. 2010, 31, 1569-1582.
11. De Ruiter, A.; Oostenbrink, C. Free energy calculations of protein-ligand interactions. Curr. Opin. Chem. Biol. 2011, 15, 547-552.
12. Guengerich, F. Cytochrome P450s and other enzymes in drug metabolism and toxicity. AAPS J. 2006, 8, E101-E111.
13. Stjernschantz, E.; Oostenbrink, C. Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys. J. 2010, 98, 2682-2691.
14. Aqvist, J.; Medina, C. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 1994, 7, 385-391.
15. Perić-Hassler, L.; Stjernschantz, E.; Oostenbrink, C.; Geerke, D.P. CYP 2D6 binding affinity predictions using multiple ligand and protein conformations. Int. J. Mol. Sci. 2013, 14, 24514-24530
16. Hritz, J.; Oostenbrink, C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. J. Phys. Chem. B 2009, 113, 12711-12720.
17. Rastelli, G.; Degliesposti, G.; del Rio, A.; Sgobba, M. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening. Chem. Biol. Drug Des. 2009, 73, 283-286.
18. Hritz, J.; de Ruiter, A.; Oostenbrink, C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: A combined approach of molecular dynamics and ligand docking. J. Med. Chem. 2008, 51, 7469-7477.
19. Vasanthanathan, P.; Olsen, L.; Jørgensen, F.S.; Vermeulen, N.P.E.; Oostenbrink, C. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations. Drug Metab. Dispos. 2010, 38, 1347-1354.
20. Stjernschantz, E.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N.P.E.; Oostenbrink, C. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the Linear Interaction Energy (LIE) method. J. Chem. Inf. Model. 2006, 46, 1972-1983.
21. Daura, X.; van Gunsteren, W.F.; Mark, A.E. Folding-unfolding thermodynamics of a ß-heptapeptide from equilibrium simulations. Prot. Struct. Funct. Bioinf. 1999, 34, 269-280.
22. Keller, B.; Daura, X.; van Gunsteren, W.F. Comparing geometric and kinetic cluster algorithms for molecular simulation data. J. Chem. Phys. 2010, 132, 074110.
23. Wang, J.; Wang, W.; Kollman, P.A.; Case, D.A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 2006, 25, 247-260.
24. Malde, A.K.; Zuo, L.; Breeze, M.; Stroet, M.; Poger, D.; Nair, P.C.; Oostenbrink, C.; Mark, A.E. An automated force field topology builder (ATB) and repository: Version 1.0. J. Chem. Theory Comput. 2011, 7, 4026-4037.
25. Vanommeslaeghe, K.; MacKerell, A.D. Automation of the CHARMM General Force Field (CGenFF) I: Bond perception and atom typing. J. Chem. Inf. Model. 2012, 52, 3144-3154.
26. Vanommeslaeghe, K.; Raman, E.P.; MacKerell, A.D. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges. J. Chem. Inf. Model. 2012, 52, 3155-3168.
27. Vaz, R.J.; Nayeem, A.; Santone, K.; Chandrasena, G.; Gavai, A.V. A 3D-QSAR model for CYP2D6 inhibition in the aryloxypropanolamine series. Bioorg. Med. Chem. Lett. 2005, 15, 3816-3820.
28. Yung-Chi, C.; Prusoff, W.H. Relationship between the inhibition constant (KI) and the concentration of inhibitor which causes 50 per cent inhibition (IC50) of an enzymatic reaction. Biochem. Pharmacol. 1973, 22, 3099-3108.
29. Caliper Online Product Database. Available online: http://www.caliperls.com/products/ cyp2d6-h.htm (accessed on 20 August 2013).
30. Eldridge, M.; Murray, C.; Auton, T.; Paolini, G.; Mee, R. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput. Aided Mol. Des. 1997, 11, 425-445.
31. Jones, G.; Willett, P.; Glen, R.C.; Leach, A.R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
32. Schmid, N.; Christ, C.D.; Christen, M.; Eichenberger, A.P.; van Gunsteren, W.F. Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput. Phys. Commun. 2012, 183, 890-903.
33. Lins, R.D.; Hünenberger, P.H. A new GROMOS force field for hexopyranose-based carbohydrates. J. Comput. Chem. 2005, 26, 1400-1412.
34. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Hermans, J. Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981; pp. 331-338.
35. Berendsen, H.J.C.; Postma, J.P.M.; van Gunsteren, W.F.; Di Nola, A.; Haak, J.R. Molecular-dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684-3690.
36. Ryckaert, J.P.; Ciccotti, G.; Berendsen, H. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
37. Ti roni, I.G.; Sperb, R.; Smith, P.E.; van Gunsteren, W.F. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 1995, 102, 5451-5495.
38. Heinz, T.N.; van Gunsteren, W.F.; Hunenberger, P.H. Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J. Chem. Phys. 2001, 115, 1125-1136.