A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions

Journal of Molecular Modeling

Volumn 19, Issue 11, 2013, Pages 5015-5030

  Liu, Yingtao ^a   Xu, Zhijian ^a   Yang, Zhuo ^a   Chen, Kaixian ^a   Zhu, Weiliang ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

Author keywords

hole; Halogen bonding; Knowledge based scoring function; Potential of mean forces; Protein ligand interaction

Indexed keywords

HALOGEN; LIGAND; PROTEIN;

ARTICLE; ATOM; BINDING AFFINITY; CHEMICAL BINDING; COMPARATIVE STUDY; CRYSTAL STRUCTURE; ELECTRIC POTENTIAL; HALOGEN BONDING; HYDROGEN BOND; KNOWLEDGE BASE; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN INTERACTION; PROTEIN LIGAND INTERACTION; SCORING SYSTEM;

HALOGENS; HYDROGEN BONDING; KNOWLEDGE BASES; LIGANDS; PROTEIN BINDING; PROTEINS;

EID: 84888224178     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-013-2005-7     Document Type: Article

References (70)

1. Auffinger P, Hays FA, Westhof E, Ho PS (2004) Halogen bonds in biological molecules. Proc Natl Acad Sci U S A 101:16789-16794
2. Voth AR, Khuu P, Oishi K, Ho PS (2009) Halogen bonds as orthogonal molecular interactions to hydrogen bonds. Nat Chem 1:74-79
3. Voth AR, Hays FA, Ho PS (2007) Directing macromolecular conformation through halogen bonds. Proc Natl Acad Sci U S A 104:6188-6193
4. Bertani R, Sgarbossa P, Venzo A, Lelj F, Amati M et al (2010) Halogen bonding in metal-organic-supramolecular networks. Coord Chem Rev 254:677-695
5. Cavallo G, Metrangolo P, Pilati T, Resnati G, Sansotera M et al (2010) Halogen bonding: a general route in anion recognition and coordination. Chem Soc Rev 39:3772-3783
6. Li HY, Lu YX, Liu YT, Zhu X, Liu HL et al (2012) Interplay between halogen bonds and pi-pi stacking interactions: CSD search and theoretical study. Phys Chem Chem Phys 14:9948-9955
7. Li HY, Lu YX, Wu WH, Liu YT, Peng CJ et al (2013) Noncovalent interactions in halogenated ionic liquids: theoretical study and crystallographic implications. Phys Chem Chem Phys 15:4405-4414
8. Lu Y, Liu Y, Xu Z, Li H, Liu H et al (2012) Halogen bonding for rational drug design and new drug discovery. Expert Opin Drug Discov 7:375-383
9. Lu YX, Liu YT, Li HY, Zhu X, Liu HL et al (2012) Energetic effects between halogen bonds and anion-pi or lone pair-pi interactions: a theoretical study. J Phys Chem A 116:2591-2597
10. Lu YX, Liu YT, Li HY, Zhu X, Liu HL et al (2012) Mutual influence between halogen bonds and cation-p interactions: a theoretical study. Chemphyschem 13:2154-2161
11. Lu YX, Shi T, Wang Y, Yang HY, Yan XH et al (2009) Halogen bonding-a novel interaction for rational drug design? J Med Chem 52:2854-2862
12. Lu YX, Wang Y, Zhu WL (2010) Nonbonding interactions of organic halogens in biological systems: implications for drug discovery and biomolecular design. Phys Chem Chem Phys 12:4543-4551
13. Metrangolo P, Neukirch H, Pilati T, Resnati G (2005) Halogen bonding based recognition processes: a world parallel to hydrogen bonding. Acc Chem Res 38:386-395
14. Metrangolo P, Resnati G (2008) Chemistry. Halogen versus hydrogen. Science 321:918-919
15. Parisini E, Metrangolo P, Pilati T, Resnati G, Terraneo G (2011) Halogen bonding in halocarbon-protein complexes: a structural survey. Chem Soc Rev 40:2267-2278
16. Legon AC (2010) The halogen bond: an interim perspective. Phys Chem Chem Phys 12:7736-7747
17. Xu Z, Liu Z, Chen T, Wang Z, Tian G et al (2011) Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors. J Med Chem 54:5607-5611
18. Murray JS, Riley KE, Politzer P, Clark T (2010) Directional weak intermolecular interactions: sigma-hole bonding. Aust J Chem 63:1598-1607
19. Murray JS, Lane P, Politzer P (2009) Expansion of the sigma-hole concept. J Mol Model 15:723-729
20. Politzer P, Murray JS, Concha MC (2007) Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors. J Mol Model 13:643-650
21. Politzer P, Murray JS, Clark T (2010) Halogen bonding: an electrostatically-driven highly directional noncovalent interaction. Phys Chem Chem Phys 12:7748-7757
22. Politzer P, Lane P, Concha MC, Ma Y, Murray JS (2007) An overview of halogen bonding. J Mol Model 13:305-311
23. Bissantz C, Kuhn B, Stahl M (2010) A medicinal chemist's guide to molecular interactions. J Med Chem 53:5061-5084
24. Merino A, Bronowska AK, Jackson DB, Cahill DJ (2010) Drug profiling: knowing where it hits. Drug Discov Today 15:749-756
25. Kubota H, Avarbock MR, Brinster RL (2004) Growth factors essential for self-renewal and expansion of mouse spermatogonial stem cells. Proc Natl Acad Sci U S A 101:16489-16494
26. Hernandes MZ, Cavalcanti SM, Moreira DR, de Azevedo Junior WF, Leite AC (2010) Halogen atoms in the modern medicinal chemistry: hints for the drug design. Curr Drug Targets 11:303-314
27. Dobes P, Rezac J, Fanfrlik J, Otyepka M, Hobza P (2011) Semiempirical quantum mechanical method PM6-DH2X describes the geometry and energetics of CK2-inhibitor complexes involving halogen bonds well, while the empirical potential fails. J Phys Chem B 115:8581-8589
28. Ibrahim MA (2012) AMBER empirical potential describes the geometry and energy of noncovalent halogen interactions better than advanced semiempirical quantum mechanical method PM6-DH2X. J Phys Chem B 116:3659-3669
29. Ibrahim MAA (2012) Molecular mechanical perspective on halogen bonding. J Mol Model 18:4625-4638
30. Ibrahim MAA (2011) Molecular mechanical study of halogen bonding in drug discovery. J Comput Chem 32:2564-2574
31. Kolar M, Hobza P (2012) On extension of the current biomolecular empirical force field for the description of halogen bonds. J Chem Theory Comput 8:1325-1333
32. Ibrahim MAA (2011) Performance assessment of semiempirical molecular orbital methods in describing halogen bonding: quantum mechanical and quantum mechanical/molecular mechanical-molecular dynamics study. J Chem Inf Model 51:2549-2559
33. Jorgensen WL, Schyman P (2012) Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents. J Chem Theory Comput 8:3895-3901
34. Kolar M, Hobza P, Bronowska AK (2013) Plugging the explicit sigma-holes in molecular docking. Chem Commun 49:981-983
35. Carter M, Rappe AK, Ho PS (2012) Scalable anisotroplic shape and electrostatic models for biological bromine halogen bonds. J Chem Theory Comput 8:2461-2473
36. Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55:620-634
37. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol 161:269-288
38. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748
39. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19:1639-1662
40. Jain AN (1996) Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 10:427-440
41. Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47:1750-1759
42. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ et al (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47:1739-1749
43. Wang RX, Lai LH, Wang SM (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16:11-26
44. Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR et al (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49:6177-6196
45. Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP (1997) 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 11:425-445
46. Bohm HJ (1994) The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 8:243-256
47. Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Arthurs S et al (2000) Deciphering common failures in molecular docking of ligand-protein complexes. J Comput Aided Mol Des 14:731-751
48. Velec HF, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48:6296-6303
49. Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42:791-804
50. Huang SY, Zou X (2006) An iterative knowledge-based scoring function to predict protein-ligand interactions: I. Derivation of interaction potentials. J Comput Chem 27:1866-1875
51. Huang SY, Zou X (2006) An iterative knowledge-based scoring function to predict protein-ligand interactions: II. Validation of the scoring function. J Comput Chem 27:1876-1882
52. Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295:337-356
53. Gohlke H, Hendlich M, Klebe G (2000) Predicting binding modes, binding affinities and 'hot spots' for protein-ligand complexes using a knowledge-based scoring function. Perspect Drug Discov 20:115-144
54. Clark T, Hennemann M, Murray JS, Politzer P (2007) Halogen bonding: the sigma-hole. Proceedings of "Modeling interactions in biomolecules II", Prague, September 5th-9th, 2005. J Mol Model 13:291-296
55. Politzer P, Murray JS, Clark T (2013) Halogen bonding and other sigma-hole interactions: a perspective. Phys Chem Chem Phys 15:11178-11189
56. Rendine S, Pieraccini S, Forni A, Sironi M (2011) Halogen bonding in ligand-receptor systems in the framework of classical force fields. Phys Chem Chem Phys 13:19508-19516
57. Zheng M, Xiong B, Luo C, Li S, Liu X et al (2011) Knowledge-based scoring functions in drug design: 3. A two-dimensional knowledge-based hydrogen-bonding potential for the prediction of protein-ligand interactions. J Chem Inf Model 51:2994-3004
58. Thomas PD, Dill KA (1996) Statistical potentials extracted from protein structures: how accurate are they? J Mol Biol 257:457-469
59. Thomas PD, Dill KA (1996) An iterative method for extracting energy-like quantities from protein structures. Proc Natl Acad Sci U S A 93:11628-11633
60. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN et al (2000) The protein data bank. Nucleic Acids Res 28:235-242
61. O'Boyle NM, Banck M, James CA, Morley C, Vandermeersch T et al (2011) Open babel: an open chemical toolbox. J Cheminform 3:33
62. Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30:2785-2791
63. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C et al (1984) A new force-field for molecular mechanical simulation of nucleic-acids and proteins. J Am Chem Soc 106:765-784
64. Wang RX, Fang XL, Lu YP, Wang SM (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47:2977-2980
65. Wang RX, Fang XL, Lu YP, Yang CY, Wang SM (2005) The PDBbind database: methodologies and updates. J Med Chem 48:4111-4119
66. Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 15:411-428
67. Lang PT, Brozell SR, Mukherjee S, Pettersen EF, Meng EC et al (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. Rna 15:1219-1230
68. Cheng TJ, Li X, Li Y, Liu ZH, Wang RX (2009) Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 49:1079-1093
69. Krammer A, Kirchhoff PD, Jiang X, Venkatachalam CM, Waldman M (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 23:395-407
70. Muegge IA (2006) PMF scoring revisited. J Med Chem 49:5895-5902