The use of chlorobenzene as a probe molecule in molecular dynamics simulations

Journal of Chemical Information and Modeling

Volumn 54, Issue 7, 2014, Pages 1821-1827

  Tan, Yaw Sing ^a,b   Spring, David R ^a   Abell, Chris ^a   Verma, Chandra ^b,c,d  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b BIOINFORMATICS INSTITUTE   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; MOLECULES; PROBES; PROTEINS;

HYDROPHOBIC BINDING; LIGAND-BINDING SITES; MOLECULAR DYNAMICS SIMULATIONS; PROBE MOLECULES; PROTEIN SURFACE;

MOLECULAR DYNAMICS;

CHLOROBENZENE; MOLECULAR PROBE; PROTEIN;

BINDING SITE; CHEMISTRY; DRUG DEVELOPMENT; MOLECULAR DYNAMICS; MOLECULAR PROBE; PROTEIN CONFORMATION;

BINDING SITES; CHLOROBENZENES; DRUG DISCOVERY; MOLECULAR DYNAMICS SIMULATION; MOLECULAR PROBES; PROTEIN CONFORMATION; PROTEINS;

EID: 84905004294     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci500215x     Document Type: Article

References (55)

1. Hernandes, M. Z.; Cavalcanti, S. M. T.; Moreira, D. R. M.; de Azevedo, W. F., Jr.; Lima Leite, A. C. Halogen atoms in the modern medicinal chemistry: hints for the drug design Curr. Drug Targets 2010, 11, 303-314
2. Gerebtzoff, G.; Li-Blatter, X.; Fischer, H.; Frentzel, A.; Seelig, A. Halogenation of drugs enhances membrane binding and permeation ChemBioChem 2004, 5, 676-684
3. Gentry, C. L.; Egleton, R. D.; Gillespie, T.; Abbruscato, T. J.; Bechowski, H. B.; Hruby, V. J.; Davis, T. P. The effect of halogenation on blood-brain barrier permeability of a novel peptide drug Peptides 1999, 20, 1229-1238
4. Metrangolo, P.; Resnati, G. Halogen bonding: a paradigm in supramolecular chemistry Chem.-Eur. J. 2001, 7, 2511-2519
5. Clark, T.; Hennemann, M.; Murray, J. S.; Politzer, P. Halogen bonding: the sigma-hole J. Mol. Model. 2007, 13, 291-296
6. Metrangolo, P.; Neukirch, H.; Pilati, T.; Resnati, G. Halogen bonding based recognition processes: a world parallel to hydrogen bonding Acc. Chem. Res. 2005, 38, 386-395
7. Wilcken, R.; Zimmermann, M. O.; Lange, A.; Joerger, A. C.; Boeckler, F. M. Principles and applications of halogen bonding in medicinal chemistry and chemical biology J. Med. Chem. 2013, 56, 1363-1388
8. Xu, Z.; Liu, Z.; Chen, T.; Chen, T.; Wang, Z.; Tian, G.; Shi, J.; Wang, X.; Lu, Y.; Yan, X.; Wang, G.; Jiang, H.; Chen, K.; Wang, S.; Xu, Y.; Shen, J.; Zhu, W. Utilization of halogen bond in lead optimization: a case study of rational design of potent phosphodiesterase type 5 (PDE5) inhibitors J. Med. Chem. 2011, 54, 5607-5611
9. Hardegger, L. A.; Kuhn, B.; Spinnler, B.; Anselm, L.; Ecabert, R.; Stihle, M.; Gsell, B.; Thoma, R.; Diez, J.; Benz, J.; Plancher, J.-M.; Hartmann, G.; Banner, D. W.; Haap, W.; Diederich, F. Systematic investigation of halogen bonding in protein-ligand interactions Angew. Chem., Int. Ed. 2011, 50, 314-318
10. Rohde, L. A. H.; Ahring, P. K.; Jensen, M. L.; Nielsen, E. O.; Peters, D.; Helgstrand, C.; Krintel, C.; Harpsoe, K.; Gajhede, M.; Kastrup, J. S.; Balle, T. Intersubunit bridge formation governs agonist efficacy at nicotinic acetylcholine α42 receptors: unique role of halogen bonding revealed J. Biol. Chem. 2012, 287, 4248-4259
11. Mattos, C.; Ringe, D. Locating and characterizing binding sites on proteins Nat. Biotechnol. 1996, 14, 595-599
12. Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules J. Med. Chem. 1985, 28, 849-857
13. Miranker, A.; Karplus, M. Functionality maps of binding sites: a multiple copy simultaneous search method Proteins 1991, 11, 29-34
14. Brenke, R.; Kozakov, D.; Chuang, G.-Y.; Beglov, D.; Hall, D.; Landon, M. R.; Mattos, C.; Vajda, S. Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques Bioinformatics 2009, 25, 621-627
15. Ivetac, A.; McCammon, J. A. Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach Chem. Biol. Drug Des. 2010, 76, 201-217
16. Seco, J.; Luque, F. J.; Barril, X. Binding site detection and druggability index from first principles J. Med. Chem. 2009, 52, 2363-2371
17. Guvench, O.; MacKerell, A. D., Jr. Computational fragment-based binding site identification by ligand competitive saturation PLoS Comp. Biol. 2009, 5, e1000435
18. Lexa, K. W.; Carlson, H. A. Full protein flexibility is essential for proper hot-spot mapping J. Am. Chem. Soc. 2011, 133, 200-202
19. Bakan, A.; Nevins, N.; Lakdawala, A. S.; Bahar, I. Druggability assessment of allosteric proteins by dynamics simulations in the presence of probe molecules J. Chem. Theory Comput. 2012, 8, 2435-2447
20. Tan, Y. S.; Sledz, P.; Lang, S.; Stubbs, C. J.; Spring, D. R.; Abell, C.; Best, R. B. Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1 Angew. Chem., Int. Ed. 2012, 51, 10078-10081
21. Zhu, M.; De Simone, A.; Schenk, D.; Toth, G.; Dobson, C. M.; Vendruscolo, M. Identification of small-molecule binding pockets in the soluble monomeric form of the A42 peptide J. Chem. Phys. 2013, 139, 035101
22. Basse, M. J.; Betzi, S.; Bourgeas, R.; Bouzidi, S.; Chetrit, B.; Hamon, V.; Morelli, X.; Roche, P. 2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions Nucleic Acids Res. 2013, 41, D824-D827
23. Xu, Z.; Yang, Z.; Liu, Y.; Lu, Y.; Chen, K.; Zhu, W. Halogen bond: its role beyond drug-target binding affinity for drug discovery and development J. Chem. Inf. Model. 2014, 54, 69-78
24. Foster, T. J.; Mackerell, A. D., Jr.; Guvench, O. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery J. Comput. Chem. 2012, 33, 1880-91
25. Kussie, P. H.; Gorina, S.; Marechal, V.; Elenbaas, B.; Moreau, J.; Levine, A. J.; Pavletich, N. P. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain Science 1996, 274, 948-953
26. Grasberger, B. L.; Lu, T. B.; Schubert, C.; Parks, D. J.; Carver, T. E.; Koblish, H. K.; Cummings, M. D.; LaFrance, L. V.; Milkiewicz, K. L.; Calvo, R. R.; Maguire, D.; Lattanze, J.; Franks, C. F.; Zhao, S. Y.; Ramachandren, K.; Bylebyl, G. R.; Zhang, M.; Manthey, C. L.; Petrella, E. C.; Pantoliano, M. W.; Deckman, I. C.; Spurlino, J. C.; Maroney, A. C.; Tomczuk, B. E.; Molloy, C. J.; Bone, R. F. Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells J. Med. Chem. 2005, 48, 909-912
27. Vassilev, L. T.; Vu, B. T.; Graves, B.; Carvajal, D.; Podlaski, F.; Filipovic, Z.; Kong, N.; Kammlott, U.; Lukacs, C.; Klein, C.; Fotouhi, N.; Liu, E. A. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2 Science 2004, 303, 844-848
28. Bista, M.; Wolf, S.; Khoury, K.; Kowalska, K.; Huang, Y.; Wrona, E.; Arciniega, M.; Popowicz, G. M.; Holak, T. A.; Domling, A. Transient protein states in designing inhibitors of the MDM2-p53 interaction Structure 2013, 21, 2143-2151
29. Baek, S.; Kutchukian, P. S.; Verdine, G. L.; Huber, R.; Holak, T. A.; Lee, K. W.; Popowicz, G. M. Structure of the stapled p53 peptide bound to Mdm2 J. Am. Chem. Soc. 2012, 134, 103-106
30. Miyazaki, M.; Naito, H.; Sugimoto, Y.; Yoshida, K.; Kawato, H.; Okayama, T.; Shimizu, H.; Miyazaki, M.; Kitagawa, M.; Seki, T.; Fukutake, S.; Shiose, Y.; Aonuma, M.; Soga, T. Synthesis and evaluation of novel orally active p53-MDM2 interaction inhibitors Biorg. Med. Chem. 2013, 21, 4319-4331
31. de Turiso, F. G.-L.; Sun, D.; Rew, Y.; Bartberger, M. D.; Beck, H. P.; Canon, J.; Chen, A.; Chow, D.; Correll, T. L.; Huang, X.; Julian, L. D.; Kayser, F.; Lo, M.-C.; Long, A. M.; McMinn, D.; Oliner, J. D.; Osgood, T.; Powers, J. P.; Saiki, A. Y.; Schneider, S.; Shaffer, P.; Xiao, S.-H.; Yakowec, P.; Yan, X.; Ye, Q.; Yu, D.; Zhao, X.; Zhou, J.; Medina, J. C.; Olson, S. H. Rational design and binding mode duality of MDM2-p53 inhibitors J. Med. Chem. 2013, 56, 4053-4070
32. Nelson, B. H.; Willerford, D. M., Biology of the interleukin-2 receptor. In Advances in Immunology, Dixon, F. J., Ed. 1998; Vol. 70, pp 1-81.
33. Arkin, M. R.; Randal, M.; DeLano, W. L.; Hyde, J.; Luong, T. N.; Oslob, J. D.; Raphael, D. R.; Taylor, L.; Wang, J.; McDowell, R. S.; Wells, J. A.; Braisted, A. C. Binding of small molecules to an adaptive protein-protein interface Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 1603-1608
34. Braisted, A. C.; Oslob, J. D.; Delano, W. L.; Hyde, J.; McDowell, R. S.; Waal, N.; Yu, C.; Arkin, M. R.; Raimundo, B. C. Discovery of a potent small molecule IL-2 inhibitor through fragment assembly J. Am. Chem. Soc. 2003, 125, 3714-3715
35. Thanos, C. D.; Randal, M.; Wells, J. A. Potent small-molecule binding to a dynamic hot spot on IL-2 J. Am. Chem. Soc. 2003, 125, 15280-15281
36. Thanos, C. D.; DeLano, W. L.; Wells, J. A. Hot-spot mimicry of a cytokine receptor by a small molecule Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 15422-15427
37. Adams, J. M. Ways of dying: multiple pathways to apoptosis Genes Dev. 2003, 17, 2481-2495
38. Wuilleme-Toumi, S.; Robillard, N.; Gomez, P.; Moreau, P.; Le Gouill, S.; Avet-Loiseau, H.; Harousseau, J. L.; Amiot, M.; Bataille, R. Mcl-1 is overexpressed in multiple myeloma and associated with relapse and shorter survival Leukemia 2005, 19, 1248-1252
39. Boisvert-Adamo, K.; Longmate, W.; Abel, E. V.; Aplin, A. E. Mcl-1 Is Required for Melanoma Cell Resistance to Anoikis Mol. Cancer Res. 2009, 7, 549-556
40. Ding, Q.; He, X.; Xia, W.; Hsu, J.-M.; Chen, C.-T.; Li, L.-Y.; Lee, D.-F.; Yang, J.-Y.; Xie, X.; Liu, J.-C.; Hung, M.-C. Myeloid cell leukemia-1 inversely correlates with glycogen synthase kinase-3 activity and associates with poor prognosis in human breast cancer Cancer Res. 2007, 67, 4564-4571
41. Lessene, G.; Czabotar, P. E.; Colman, P. M. BCL-2 family antagonists for cancer therapy Nat. Rev. Drug Discovery 2008, 7, 989-1000
42. Friberg, A.; Vigil, D.; Zhao, B.; Daniels, R. N.; Burke, J. P.; Garcia-Barrantes, P. M.; Camper, D.; Chauder, B. A.; Lee, T.; Olejniczak, E. T.; Fesik, S. W. Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design J. Med. Chem. 2013, 56, 15-30
43. Tanaka, Y.; Aikawa, K.; Nishida, G.; Homma, M.; Sogabe, S.; Igaki, S.; Hayano, Y.; Sameshima, T.; Miyahisa, I.; Kawamoto, T.; Tawada, M.; Imai, Y.; Inazuka, M.; Cho, N.; Imaeda, Y.; Ishikawa, T. Discovery of potent Mcl-1/Bcl-xL dual inhibitors by using a hybridization strategy based on structural analysis of target proteins J. Med. Chem. 2013, 56, 9635-9645
44. Labi, V.; Erlacher, M.; Kiessling, S.; Villunger, A. BH3-only proteins in cell death initiation, malignant disease and anticancer therapy Cell Death Differ. 2006, 13, 1325-1338
45. Amundson, S. A.; Myers, T. G.; Scudiero, D.; Kitada, S.; Reed, J. C.; Fornace, A. J. An informatics approach identifying markers of chemosensitivity in human cancer cell lines Cancer Res. 2000, 60, 6101-6110
46. Muchmore, S. W.; Sattler, M.; Liang, H.; Meadows, R. P.; Harlan, J. E.; Yoon, H. S.; Nettesheim, D.; Chang, B. S.; Thompson, C. B.; Wong, S. L.; Ng, S. C.; Fesik, S. W. X-ray and NMR structure of human Bcl-x(L), an inhibitor of programmed cell death Nature 1996, 381, 335-341
47. Manion, M. K.; ONeill, J. W.; Giedt, C. D.; Kim, K. M.; Zhang, K. Y. Z.; Hockenbery, D. M. Bcl-X-L mutations suppress cellular sensitivity to antimycin A J. Biol. Chem. 2004, 279, 2159-2165
48. Wysoczanski, P.; Mart, R. J.; Loveridge, E. J.; Williams, C.; Whittaker, S. B. M.; Crump, M. P.; Allemann, R. K. NMR solution structure of a photoswitchable apoptosis activating Bak peptide bound to Bcl-x(L) J. Am. Chem. Soc. 2012, 134, 7644-7647
49. Brady, R. M.; Vom, A.; Roy, M. J.; Toovey, N.; Smith, B. J.; Moss, R. M.; Hatzis, E.; Huang, D. C. S.; Parisot, J. P.; Yang, H.; Street, I. P.; Colman, P. M.; Czabotar, P. E.; Baell, J. B.; Lessene, G. De-novo designed library of benzoylureas as inhibitors of BCL-XL: synthesis, structural and biochemical characterization J. Med. Chem. 2014, 57, 1323-1343
50. Stauber, D. J.; Debler, E. W.; Horton, P. A.; Smith, K. A.; Wilson, I. A. Crystal structure of the IL-2 signaling complex: paradigm for a heterotrimeric cytokine receptor Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 2788-2793
51. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
52. Ibrahim, M. A. A. Molecular mechanical study of halogen bonding in drug discovery J. Comput. Chem. 2011, 32, 2564-2574
53. Rendine, S.; Pieraccini, S.; Forni, A.; Sironi, M. Halogen bonding in ligand-receptor systems in the framework of classical force fields Phys. Chem. Chem. Phys. 2011, 13, 19508-19516
54. Jorgensen, W. L.; Schyman, P. Treatment of halogen bonding in the OPLS-AA force field: application to potent anti-HIV agents J. Chem. Theory Comput. 2012, 8, 3895-3901
55. Du, L.; Gao, J.; Bi, F.; Wang, L.; Liu, C. A polarizable ellipsoidal force field for halogen bonds J. Comput. Chem. 2013, 34, 2032-2040