On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

Proceedings of the National Academy of Sciences of the United States of America

Volumn 109, Issue 6, 2012, Pages 1937-1942

  Wang, Lingle ^a   Berne, B J ^a   Friesner, Richard A ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

Drug design; Enhanced sampling; Lead optimization; Protein ligand binding affinity; Structural reorganization

Indexed keywords

THROMBIN;

ACCURACY; ARTICLE; BINDING AFFINITY; CONFORMATION; CRYSTAL STRUCTURE; ENERGY; LIGAND BINDING; LIQUID; PRIORITY JOURNAL; PROTEIN BINDING; QUANTITATIVE ANALYSIS; RELIABILITY; SIMULATION;

ACETAMIDES; BACTERIOPHAGE T4; BENZENE; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; LIGANDS; MODELS, MOLECULAR; MURAMIDASE; MUTANT PROTEINS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS; THROMBIN; VALINE; XYLENES;

EID: 84863137873     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1114017109     Document Type: Article

References (27)

1. Mobley DL, Dill KA (2009) Binding of small-molecule ligands to proteins: "What you see" is not always "what you get". Structure 17:489-498.
2. Jorgensen WL (2009) Efficient drug lead discovery and optimization. Acc Chem Res 42:724-733 PMID: 19317443.
3. Gallicchio E, Levy RM (2011) Advances in all atom sampling methods for modeling protein-ligand binding affinities. Curr Opin Struct Biol 21:161-166.
4. Chodera JD, et al. (2011) Alchemical free energy methods for drug discovery: Progress and challenges. Curr Opin Struct Biol 21:150-160.
5. Jorgensen WL, Rives TJ (1988) The OPLS potential functions for proteins - energy minimizations for crystals of cyclic-peptides and crambin. J Am Chem Soc 110:1657-1666.
6. MacKerell AD, et al. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616.
7. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487. (Pubitemid 35339015)
8. Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157-1174.
9. Banks JL, et al. (2005) Integrated modeling program, applied chemical theory (impact). J Comput Chem 26:1752-1780. (Pubitemid 43076184)
10. Mobley DL, Chodera JD, Dill KA (2007) Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change. J Chem Theory Comput 3:1231-1235 PMID: 18843379.
11. Jiang W, Roux B (2010) Free energy perturbation hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theory Comput 6:2559-2565.
12. Michel J, Tirado-Rives J, Jorgensen WL (2009) Energetics of displacing water molecules from protein binding sites: Consequences for ligand optimization. J Am Chem Soc 131:15403-15411 PMID: 19778066.
13. Young T, Abel R, Kim B, Berne BJ, Friesner RA (2007) Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci USA 104:808-813. (Pubitemid 46154692)
14. Wang L, Berne BJ, Friesner RA (2011) Ligand binding to protein-binding pockets with wet and dry regions. Proc Natl Acad Sci USA 108:1326-1330.
15. Liu P, Kim B, Friesner RA, Berne BJ (2005) Replica exchange with solute tempering: A method for sampling biological systems in explicit water. Proc Natl Acad Sci USA 102:13749-13754. (Pubitemid 41377651)
16. Wang L, Friesner RA, Berne BJ (2011) Replica exchange with solute scaling: A more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115:9431-9438.
17. Moors SLC, Michielssens S, Ceulemans A (2011) Improved replica exchange method for native-state protein sampling. J Chem Theory Comput 7:231-237.
18. Morton A, Matthews BW (1995) Specificity of ligand binding in a buried nonpolar cavity of t4 lysozyme: Linkage of dynamics and structural plasticity. Biochemistry 34:8576-8588 PMID: 7612599.
19. Morton A, Baase WA, Matthews BW (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of t4 lysozyme. Biochemistry 34:8564-8575 PMID: 7612598.
20. Lumma WC, et al. (1998) Design of novel, potent, noncovalent inhibitors of thrombin with nonbasic p-1 substructures: Rapid structure-activity studies by solid-phase synthesis. J Med Chem 41:1011-1013.
21. Coughlin SR (2000) Thrombin signalling and protease-activated receptors. Nature 407:258-264.
22. Burgey CS, et al. (2003) Metabolism-directed optimization of 3-aminopyrazinone acetamide thrombin inhibitors. development of an orally bioavailable series containing p1 and p3 pyridines. J Med Chem 46:461-473. (Pubitemid 36182749)
23. Deng Y, Roux B (2006) Calculation of standard binding free energies: Aromatic molecules in the t4 lysozyme l99a mutant. J Chem Theory Comput 2:1255-1273.
24. Gallicchio E, Lapelosa M, Levy RM (2010) Binding energy distribution analysis method (bedam) for estimation of protein-ligand binding affinities. J Chem Theory Comput 6:2961-2977.
25. Min D, Li H, Li G, Bitetti-Putzer R, Yang W (2007) Synergistic approach to improve alchemical free energy calculation in rugged energy surface. J Chem Phys 126 144109.
26. Sherman W, Day T, Jacobson MP, Friesner RA, Farid R (2006) Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem 49:534-553. (Pubitemid 43157487)
27. Fukunishi H, Watanabe O, Takada S (2002) On the hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J Chem Phys 116:9058-9067. (Pubitemid 34631453)