The importance of protonation and tautomerization in relative binding affinity prediction: a comparison of AMBER TI and Schrödinger FEP

Journal of Computer-Aided Molecular Design

Volumn 30, Issue 7, 2016, Pages 533-539

  Hu, Yuan ^a   Sherborne, Brad ^a   Lee, Tai Sung ^b   Case, David A ^b   York, Darrin M ^b   Guo, Zhuyan ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

Free energy calculation; Free energy perturbation; Protein ligand binding affinity; Protonation; Tautomerization; Thermodynamic integration

Indexed keywords

AMBER; BINDING ENERGY; FREE ENERGY; LIGANDS;

DRUG DISCOVERY; FREE ENERGY PERTURBATION; FREE-ENERGY CALCULATIONS; PROTEIN-LIGAND BINDING AFFINITIES; PROTONATION STATE; PROTONATIONS; RELATIVE BINDING AFFINITY; RUTGERS; TAUTOMERIZATIONS; THERMODYNAMIC INTEGRATION;

PROTONATION;

BLOOD CLOTTING FACTOR 10A INHIBITOR; LIGAND; POLITEF; PROTEIN BINDING; PROTON;

AMBER THERMODYNAMIC INTEGRATION; ARTICLE; CALCULATION; DRUG BINDING; DRUG DESIGN; DRUG STRUCTURE; IMAGING SOFTWARE; INTERMETHOD COMPARISON; LIGAND BINDING; PRIORITY JOURNAL; PROTON TRANSPORT; RELATIVE BINDING AFFINITY; SCHRODINGER FREE ENERGY PERTURBATION; TAUTOMERIZATION; CHEMISTRY; DRUG DEVELOPMENT; HUMAN; MOLECULAR MODEL; THERMODYNAMICS;

DRUG DESIGN; DRUG DISCOVERY; HUMANS; LIGANDS; MODELS, MOLECULAR; POLYTETRAFLUOROETHYLENE; PROTEIN BINDING; PROTONS; THERMODYNAMICS;

EID: 84982844561     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-016-9920-5     Document Type: Article

References (30)

1. Lovering F, Aevazelis C, Chang J, Dehnhardt C, Fitz L, Han S, Janz K, Lee J, Kaila N, McDonald J, Moore W (2016) Imidazotriazines: spleen tyrosine kinase (Syk) inhibitors identified by free-energy perturbation (FEP). ChemMedChem 11:217–233
2. Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL (2015) Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field. J Am Chem Soc 137:2695–2703
3. Armacost KA, Goh GB, Brooks CL III (2015) Biasing potential replica exchange multisite λ-dynamics for efficient free energy calculations. J Chem Theory Comput 11:1267–1277
4. 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
5. Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS (2011) Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol 21:150–160
6. Michel J, Essex JW (2010) Prediction of protein–ligand binding affinity by free energy simulations: assumptions pitfalls and expectations. J Comput Aided Mol Des 24:639–658
7. Jorgensen WL, Tirado-Rives J (2005) Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J Comput Chem 26:1689–1700
8. Loeffler HH, Michel J, Woods C (2015) FESetup: automating setup for alchemical free energy simulations. J Chem Inf Model 55:2485–2490
9. Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL (2013) Lead optimization mapper: automating free energy calculations for lead optimization. J Comput Aided Mol Des 27:755–770
10. Klimovich PV, Shirts MR, Mobley DL (2015) Guidelines for the analysis of free energy calculations. J Comput Aided Mol Des 29:397–411
11. Klimovich PV, Shirts MR, Mobley DL (2015) A Python tool to set up relative free energy calculations in GROMACS. J Comput Aided Mol Des 29:1007–1014
12. Gapsys V, Michielssens S, Seeliger D, de Groot BL (2015) pmx: automated protein structure and topology generation for alchemical perturbations. J Comput Chem 36:348–354
13. Sadiq SK, Wright D, Watson SJ, Zasada SJ, Stoica I, Coveney PV (2008) Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases. J Chem Inf Model 48:1909–1919
14. Homeyer N, Gohlke H (2013) FEW: a workflow tool for free energy calculations of ligand binding. J Comput Chem 34:965–973
15. Homeyer N, Gohlke H (2015) Extension of the free energy workflow FEW towards implicit solvent/implicit membrane MM–PBSA calculations. Biochim Biophys Acta Gen Subj 1850:972–982
16. Liao CZ, Nicklaus MC (2009) Comparison of nine programs predicting pK(a) values of pharmaceutical substances. J Chem Inf Model 49:2801–2812
17. Meloun M, Bordovska S (2007) Benchmarking and validating algorithms that estimate pK(a) values of drugs based on their molecular structures. Anal Bioanal Chem 389:1267–1281
18. Pinto DJ, Orwat MJ, Wang S, Fevig JM, Quan ML, Amparo E, Cacciola J, Rossi KA, Alexander RS, Smallwood AM, Luettgen JM (2001) Discovery of 1-[3-(Amino-methyl) phenyl]-N-[3-fluoro-2′-(methylsulfonyl)-[11′-biphenyl]-4-yl]-3-(trifluoromethyl)-1 H-pyrazole-5-carboxamide (DPC423) a highly potent selective and orally bioavailable inhibitor of blood coagulation factor Xa 1. J Med Chem 44:566–578
19. Case DA, Berryman JT, Betz RM, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Luchko T, Luo R, Madej B, Merz KM, Monard G, Needham P, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe, Roitberg A, Salomon-Ferrer R, Simmerling CL, Smith W, Swails J, Walker RC, Wang J, Wolf RM, Wu X, York DM, Kollman PA (2015) AMBER 2015. University of California, San Francisco
20. Wang J, Wolf R, Caldwell J, Kollamn P, Case D (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174
21. Jakalian A, Bush B, Jack D, Bayly C (2000) Fast efficient generation of high-quality atomic charges AM1-BCC model: I Method. J Comput Chem 21:132–146
22. Jakalian A, Jack D, Bayly C (2002) Fast efficient generation of high-quality atomic charges AM1-BCC model: II parameterization and validation. J Comput Chem 23:1623–1641
23. Steinbrecher T, Joung I, Case DA (2011) Soft-core potentials in thermodynamic integration: comparing one and two-step transformations. J Comput Chem 32:3253–3263
24. Desmond Molecular Dynamics System, version 4.3, D. E. Shaw Research, New York, NY, 2015. Maestro-Desmond Interoperability Tools, version 4.3, Schrödinger, New York, NY, 2015
25. Zwanzig RW (1954) High-temperature equation of state by a perturbation method I nonpolar gases. J Chem Phys 22:1420–1426
26. Storer J, Giesen D, Cramer C, Truhlar D (1995) Class IV charge models: a new semiempirical approach in quantum chemistry. J Comput Aided Mol Des 9:87–110
27. Liu P, Kim B, Friesner RA, Berne B (2005) Replica exchange with solute tempering: a method for sampling biological systems in explicit water. J Proc Natl Acad Sci USA 102:13749–13754
28. Wang L, Berne BJ, Friesner RA (2012) On achieving high accuracy and reliability in the calculation of relative protein–ligand binding affinities. Proc Natl Acad Sci USA 109:1937–1942
29. Wang L, Lin T, Abel R, Schrödinger LLc (2013) Cycle closure estimation of relative binding affinities and errors. US Patent Application 13/840039
30. Case DA, Betz RM, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Lin C, Luchko T, Luo R, Madej B, Mermelstein D, Merz KM, Monard G, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Sagui C, Simmerling CL, Botello-Smith WM, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Xiao L, Kollman PA (2016) AMBER 2016. University of California, San Francisco