Structural modeling of HLA-B*1502/peptide/carbamazepine/T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis

References

• Arfeen, M., Patel, R., Khan, T., & Bharatam, P. V. (in press). Molecular dynamics simulation studies of GSK-3β ATP competitive inhibitors: Understanding the factors contributing to selectivity. Journal of Biomolecular Structure and Dynamics. doi:10.1080/07391102.2015.1063457
   PubMed Web of Science ®Google Scholar
• Balasco, N., Barone, D., & Vitagliano, L. (2015). Structural conversion of the transformer protein RfaH: New insights derived from protein structure prediction and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 33, 2173–2179. doi:10.1080/07391102.2014.994188
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242. doi:10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Besler, B. H., Merz, K. M., Jr., & Kollman, P. A. (1990). Atomic charges derived from semiempirical methods. Journal of Computational Chemistry, 11, 431–439. doi:10.1002/jcc.540110404
   Web of Science ®Google Scholar
• Bharadwaj, M., Illing, P., & Kostenko, L. (2010). Personalized medicine for HLA-associated drug-hypersensitivity reactions. Personalized Medicine, 7, 495–516. doi:10.2217/pme.10.46
   Web of Science ®Google Scholar
• Bharadwaj, M., Illing, P., Theodossis, A., Purcell, A. W., Rossjohn, J., & McCluskey, J. (2012). Drug hypersensitivity and human leukocyte antigens of the major histocompatibility complex. Annual Review of Pharmacology and Toxicology, 52, 401–431. doi:10.1146/annurev-pharmtox-010611-134701
   PubMed Web of Science ®Google Scholar
• Bond, C. A., & Raehl, C. L. (2006). Adverse drug reactions in United States hospitals. Pharmacotherapy, 26, 601–608. doi:10.1592/phco.26.5.601
   PubMed Web of Science ®Google Scholar
• Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688. doi:10.1002/jcc.20290
   PubMed Web of Science ®Google Scholar
• Chen, P., Lin, J. J., Lu, C. S., Ong, C. T., Hsieh, P. F., Yang, C. C., … Shen, C. Y (2011). Carbamazepine-induced toxic effects and HLA-B*1502 screening in Taiwan. New England Journal of Medicine, 364, 1126–1133. doi:10.1056/nejmoa1009717
   PubMed Web of Science ®Google Scholar
• Chessman, D., Kostenko, L., Lethborg, T., Purcell, A. W., Williamson, N. A., Chen, Z., … McCluskey, J. (2008). Human leukocyte antigen class I-restricted activation of CD8+ T cells provides the immunogenetic basis of a systemic drug hypersensitivity. Immunity, 28, 822–832. doi:10.1016/j.immuni.2008.04.020
   PubMed Web of Science ®Google Scholar
• Chung, W. H., & Hung, S. I. (2012). Recent advances in the genetics and immunology of Stevens-Johnson syndrome and toxic epidermal necrosis. Journal of Dermatological Science, 66, 190–196. doi:10.1016/j.jdermsci.2012.04.002
   PubMed Web of Science ®Google Scholar
• Chung, W. H., Hung, S. I., Hong, H. S., Hsih, M. S., Yang, L. C., Ho, H. C., … Chen, Y. T. (2004). Medical genetics: A marker for Stevens–Johnson syndrome. Nature, 428, 486. doi:10.1038/428486a
   PubMed Web of Science ®Google Scholar
• Daly, A. K., Donaldson, P. T., Bhatnagar, P., Shen, Y., Pe'er, I., Floratos, A., … Day, C. P. (2009). HLA-B*5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nature Genetics, 41, 816–819. doi:10.1038/ng.379
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092. doi:10.1063/1.464397
   Web of Science ®Google Scholar
• Fan, J. R., Zheng, Q. C., Cui, Y. L., Li, W. K., & Zhang, H. X. (2015) Investigation of ligand selectivity in CYP3A7 by molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 33, 2360–2367. doi:10.1080/07391102.2015.1054884
   PubMed Web of Science ®Google Scholar
• Gasteiger, J., & Marsili, M. (1996). Iterative partial equalization of orbital electronegativity – A rapid access to atomic charges. Tetrahedron, 36, 3219–3228. doi:10.1016/0040-4020(80)80168-2
   Web of Science ®Google Scholar
• Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of Computational Chemistry, 17, 490–519. doi:10.1002/(sici)1096-987x(199604)17
   Web of Science ®Google Scholar
• Hung, S. I., Chung, W. H., Jee, S. H., Chen, W. C., Chang, Y. T., Lee, W. R., … Chen, Y. T. (2006). Genetic susceptibility to carbamazepine-induced cutaneous adverse drug reactions. Pharmacogenetics and Genomics, 16, 297–306. doi:10.1097/01.fpc.0000199500.46842.4a
   PubMed Web of Science ®Google Scholar
• Hung, S. I., Chung, W. H., Liou, L. B., Chu, C. C., Lin, M., Huang, H. P., … Chen, Y. T. (2005). HLA-B*5801 allele as a genetic marker for severe cutaneous adverse reactions caused by allopurinol. Proceedings of the National Academy of Sciences, 102, 4134–4139. doi:10.1073/pnas.0409500102
   PubMed Web of Science ®Google Scholar
• Illing, P. T., Vivian, J. P., Dudek, N. L., Kostenko, L., Chen, Z., Bharadwaj, M., … McCluskey, J. (2012). Immune self-reactivity triggered by drug-modified HLA-peptide repertoire. Nature, 486, 554–558. doi:10.1038/nature11147
   PubMed Web of Science ®Google Scholar
• Illing, P. T., Vivian, J. P., Purcell, A. W., Rossjohn, J., & McCluskey, J. (2013). Human leukocyte antigen-associated drug hypersensitivity. Current Opinion in Immunology, 25, 81–89. doi:10.1016/j.coi.2012.10.002
   PubMed Web of Science ®Google Scholar
• Jakalian, A., Jack, D. B., & Bayly, C. I. (2002). Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. Journal of Computational Chemistry, 23, 1623–1641. doi:10.1002/jcc.10128
   PubMed Web of Science ®Google Scholar
• Johnson, J. A., & Bootman, J. L. (1995). Drug-related morbidity and mortality. Archives of Internal Medicine, 155, 1949–1956. doi:10.1001/archinte.155.18.1949
   PubMed Web of Science ®Google Scholar
• Knapp, B., Omasits, U., & Schreiner, W. (2008). Side chain substitution benchmark for peptide/MHC interaction. Protein Science, 17, 977–982. doi:10.1110/ps.073402508
   PubMed Web of Science ®Google Scholar
• Ko, T. M., Chung, W. H., Wei, C. Y., Shih, H. Y., Chen, J. K., Lin, C. H., … Hung, S. I. (2011). Shared and restricted T-cell receptor use is crucial for carbamazepine-induced Stevens-Johnson syndrome. Journal of Allergy and Clinical Immunology, 128, 1266–1276. doi:10.1016/j.jaci.2011.08.013
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., … Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33, 889–897. doi:10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Krivov, G. G., Shapovalov, M. V., & Dunbrack, R. L., Jr. (2009). Improved prediction of protein side-chain conformations with SCWRL4. Proteins: Structure, Function, and Bioinformatics, 77, 778–795. doi:10.1002/prot.22488
   PubMed Web of Science ®Google Scholar
• Mallal, S., Nolan, D., Witt, C., Masel, G., Martin, A. M., Moore, C., … Christiansen, F. T. (2002). Association between presence of HLA-B*5701, HLA-DR7, and HLA-DQ3 and hypersensitivity to HIV-1 reverse-transcriptase inhibitor abacavir. The Lancet, 359, 727–732. doi:10.1016/s0140-6736(02)07873-x
   PubMed Web of Science ®Google Scholar
• Martin, A. C. R. (1982). Rapid comparison of protein structures. Acta Crystallographica Section A, 38, 871–873. doi:10.1107/s0567739482001806
   Web of Science ®Google Scholar
• Martí-Renom, M. A., Stuart, A. C., Fiser, A., Sánchez, R., Melo, F., & Šali, A. (2000). Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure, 29, 291–325. doi:10.1146/annurev.biophys.29.1.291
   PubMedGoogle Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30, 2785–2791. doi:10.1002/jcc.21256
   PubMed Web of Science ®Google Scholar
• Ngan, C. H., Bohnuud, T., Mottarella, S. E., Beglov, D., Villar, E. A., Hall, D. R., … Vajda, S. (2012). FTMAP: Extended protein mapping with user-selected probe molecules. Nucleic Acids Research, 40, W271–W275. doi:10.1093/nar/gks441
   Google Scholar
• Norcross, M. A., Luo, S., Lu, L., Boyne, M. T., Gomarteli, M., Rennels, A. D., … Buchli, R. (2012). Abacavir induces loading of novel self-peptides into HLA-B*57. AIDS, 26, F21–F29. doi:10.1097/qad.0b013e328355fe8f
   PubMed Web of Science ®Google Scholar
• Ostrov, D. A., Grant, B. J., Pompeu, Y. A., Sidney, J., Harndahl, M., Southwood, S., … Peter,B. (2012). Drug hypersensitivity caused by alteration of the MHC-presented self-peptide repertoire. Proceedings of the National Academy of Sciences, 109, 9959–9964. doi:10.1073/pnas.1207934109
   PubMed Web of Science ®Google Scholar
• Pirmohamed, M., Breckenridge, A. M., Kitteringham, N. R., & Park, B. K. (1998). Fortnightly review: Adverse drug reactions. BMJ, 316, 1295–1298. doi:10.1136/bmj.316.7140.1295
   PubMed Web of Science ®Google Scholar
• Pirmohamed, M., Naisbitt, D. J., Gordon, F., & Park, B. K. (2002). The danger hypothesis – Potential role in idiosyncratic drug reactions. Toxicology, 181–182, 55–63. doi:10.1016/s0300-483x(02)00255-x
   PubMed Web of Science ®Google Scholar
• Pompeu, Y. A., Stewart, J. D., Mallal, S., Phillips, E., Peters, B., & Ostrov, D. A. (2012). The structural basis of HLA-associated drug hypersensitivity syndromes. Immunological Reviews, 250, 158–166. doi:10.1111/j.1600-065x.2012.01163.x
   PubMed Web of Science ®Google Scholar
• Rocchia, W., Alexov, E., & Honig, B. (2001). Extending the applicability of the nonlinear Poisson-Boltzmann Equation: Multiple dielectric constants and multivalent ions. The Journal of Physical Chemistry B, 105, 6507–6514. doi:10.1021/jp010454y
   Web of Science ®Google Scholar
• Ryckaert, J., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23, 327–341. doi:10.1016/0021-9991(77)90098-5
   Web of Science ®Google Scholar
• Sitkoff, D., Sharp, K. A., & Honig, B. (1994). Accurate calculation of hydration free-energies using macroscopic solvent models. The Journal of Physical Chemistry, 98, 1978–1988. doi:10.1021/j100058a043
   Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25, 247–260. doi:10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157–1174. doi:10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Wei, C. Y., Chung, W. H., Huang, H. W., Chen, Y. T., & Hung, S. I. (2012). Direct interaction between HLA-B and carbamazepine activates T cells in patients with Stevens-Johnson syndrome. Journal of Allergy and Clinical Immunology, 129, 1562–1569. doi:10.1016/j.jaci.2011.12.990
   PubMed Web of Science ®Google Scholar
• Wu, X. W., & Brooks, B. R. (2003). Self-guided Langevin dynamics simulation method. Chemical Physics Letters, 381, 512–518. doi:10.1016/j.cplett.2003.10.013
   Web of Science ®Google Scholar
• Yang, C. W., Hung, S. I., Juo, C. G., Lin, Y. P., Fang, W. H., Lu, I. H., … Chen, Y. T. (2007). HLA-B∗1502–bound peptides: Implications for the pathogenesis of carbamazepine-induced Stevens-Johnson syndrome. Journal of Allergy and Clinical Immunology, 120, 870–877. doi:10.1016/j.jaci.2007.06.017
   PubMed Web of Science ®Google Scholar
• Yang, C., Wang, C., Zhang, S., Huang, J., & Zhou, P. (2015). Structural and energetic insights into the intermolecular interaction among human leukocyte antigens, clinical hypersensitive drugs and antigenic peptides. Molecular Simulation, 41, 7418–7751. doi:10.1080/08927022.2014.929127
   Web of Science ®Google Scholar
• Zhou, P., Huang, J., & Tian, F. (2012). Specific noncovalent interactions at protein-ligand interface: Implications for rational drug design. Current Medicinal Chemistry, 19, 226–238. doi:10.2174/092986712803414150
   PubMed Web of Science ®Google Scholar
• Zhou, P., Wang, C., Ren, Y., Yang, C., & Tian, F. (2013). Computational peptidology: A new and promising approach to therapeutic peptide design. Current Medicinal Chemistry, 20, 1985–1996. doi:10.2174/0929867311320150005
   PubMed Web of Science ®Google Scholar
• Zhou, P., Yang, C., Ren, Y., Wang, C., & Tian, F. (2013). What are the ideal properties for functional food peptides with antihypertensive effect? A computational peptidology approach. Food Chemistry, 141, 2967–2973. doi:10.1016/j.foodchem.2013.05.140
   PubMed Web of Science ®Google Scholar