Abstract
Aim:
To investigate the molecular mechanisms underlying the influence of DNA polymerase from different genotypes of hepatitis B virus (HBV) on the binding affinity of adefovir (ADV).
Methods:
Computational approaches, including homology modeling, docking, MD simulation and MM/PBSA free energy analyses were used.
Results:
Sequence analyses revealed that residue 238 near the binding pocket was not only a polymorphic site but also a genotype-specific site (His238 in genotype B; Asn238 in genotype C). The calculated binding free-energy supported the hypothesis that the polymerase from HBV genotype C was more sensitive to ADV than that from genotype B. By using MD simulation trajectory analysis, binding free energy decomposition and alanine scanning, some energy variation in the residues around the binding pocket was observed. Both the alanine mutations at residues 236 and 238 led to an increase of the energy difference between genotypes C and B (ΔΔGC–B), suggesting that these residues contributed to the genotype-associated antiviral variability with regard to the interaction with ADV.
Conclusion:
The results support the hypothesis that the HBV genotype C polymerase is more sensitive to ADV than that from genotype B. Moreover, residue N236 and the polymorphic site 238 play important roles in contributing to the higher sensitivity of genotype C over B in the interaction with ADV.
Similar content being viewed by others
Log in or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Zoulim F, Parvaz P, Marcellin P, Zarski JP, Beaugrand M, Benhamou Y, et al. Adefovir dipivoxil is effective for the treatment of cirrhotic patients with lamivudine failure. Liver Int 2009; 29: 420–6.
Li XD, Wang L, Zhong YW, Wong VW, Xu ZH, Liu Y, et al. Hepatitis B virus (HBV) subgenotypes C2 and B2 differ in lamivudine- and adefovir-resistance-associated mutational patterns in HBV-infected Chinese patients. J Clin Microbiol 2010; 48: 4363–9.
Tanwar S, Dusheiko G . Is there any value to hepatitis B virus genotype analysis? Curr Gastroenterol Rep 2012; 14: 37–46.
Ma Y, Ding Y, Juan F, Dou XG . Genotyping the hepatitis B virus with a fragment of the HBV DNA polymerase gene in Shenyang, China. Virol J 2011; 8: 315.
Chu CM, Liaw YF . Genotype C hepatitis B virus infection is associated with a higher risk of reactivation of hepatitis B and progression to cirrhosis than genotype B: a longitudinal study of hepatitis B e antigen-positive patients with normal aminotransferase levels at baseline. J Hepatol 2005; 43: 411–7.
Yuen MF, Sablon E, Yuan HJ, Wong DK, Hui CK, Wong BC, et al. Significance of hepatitis B genotype in acute exacerbation, HBeAg seroconversion, cirrhosis-related complications, and hepatocellular carcinoma. Hepatology 2003; 37: 562–7.
Yang HI, Yeh SH, Chen PJ, Iloeje UH, Jen CL, Su J, et al. Associations between hepatitis B virus genotype and mutants and the risk of hepatocellular carcinoma. J Natl Cancer Inst 2008; 100: 1134–43.
Yadav V, Chu CK . Molecular mechanisms of adefovir sensitivity and resistance in HBV polymerase mutants: a molecular dynamics study. Bioorg Med Chem Lett 2004; 14: 4313–7.
Rhee SY, Margeridon-Thermet S, Nguyen MH, Liu TF, Kagan RM, Beggel B, et al. Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Antiviral Res 2010; 88: 269–75.
Sheng YJ, Liu JY, Tong SW, Hu HD, Zhang DZ, Hu P, et al. Lamivudine plus adefovir combination therapy versus entecavir monotherapy for lamivudine–resistant chronic hepatitis B: a systematic review and meta–analysis. Virol J 2011; 8: 393.
Angus P, Vaughan R, Xiong S, Yang H, Delaney W, Gibbs C, et al. Resistance to adefovir dipivoxil therapy associated with the selection of a novel mutation in the HBV polymerase. Gastroenterology 2003; 125: 292–7.
Kao JH, Chen PJ, Lai MY, Chen DS . Hepatitis B genotypes correlate with clinical outcomes in patients with chronic hepatitis B. Gastroenterology 2000; 118: 554–9.
Kao JH, Wu NH, Chen PJ, Lai MY, Chen DS . Hepatitis B genotypes and the response to interferon therapy. J Hepatol 2000; 33: 998–1002.
Erhardt A, Reineke U, Blondin D, Gerlich WH, Adams O, Heintges T, et al. Mutations of the core promoter and response to interferon treatment in chronic replicative hepatitis B. Hepatology 2000; 31: 716–25.
Kobayashi M, Arase Y, Ikeda K, Tsubota A, Suzuki Y, Saitoh S, et al. Clinical characteristics of patients infected with hepatitis B virus genotypes A, B, and C. J Gastroenterol 2002; 37: 35–9.
Zollner B, Petersen J, Schafer P, Schroter M, Laufs R, Sterneck M, et al. Subtype-dependent response of hepatitis B virus during the early phase of lamivudine treatment. Clin Infect Dis 2002; 34: 1273–7.
Cooksley WG . Do we need to determine viral genotype in treating chronic hepatitis B? J Viral Hepat 2010; 17: 601–10.
Zeng AZ, Deng H, Yang C, Xin XJ, Li QL, Guo JJ, et al. Hepatitis B virus genotype-associated variability in antiviral response to adefovir dipivoxil therapy in Chinese Han population. Tohoku J Exp Med 2008; 216: 205–11.
Westland C, Delaney W 4th, Yang H, Chen SS, Marcellin P, Hadziyannis S, et al. Hepatitis B virus genotypes and virologic response in 694 patients in phase III studies of adefovir dipivoxil1. Gastroenterology 2003; 125: 107–16.
Raimondi S, Maisonneuve P, Bruno S, Mondelli MU . Is response to antiviral treatment influenced by hepatitis B virus genotype? J Hepatol 2010; 52: 441–9.
Wang X, Yang W, Xu X, Zhang H, Li Y, Wang Y . Studies of benzothiadiazine derivatives as hepatitis C virus NS5B polymerase inhibitors using 3D-QSAR, molecular docking and molecular dynamics. Curr Med Chem 2010; 17: 2788–803.
Das K, Xiong X, Yang H, Westland CE, Gibbs CS, Sarafianos SG, et al. Molecular modeling and biochemical characterization reveal the mechanism of hepatitis B virus polymerase resistance to lamivudine (3TC) and emtricitabine (FTC). J Virol 2001; 75: 4771–9.
Langley DR, Walsh AW, Baldick CJ, Eggers BJ, Rose RE, Levine SM, et al. Inhibition of hepatitis B virus polymerase by entecavir. J Virol 2007; 81: 3992–4001.
Bartholomeusz A, Tehan BG, Chalmers DK . Comparisons of the HBV and HIV polymerase, and antiviral resistance mutations. Antivir Ther 2004; 9: 149–60.
Daga PR, Duan J, Doerksen RJ . Computational model of hepatitis B virus DNA polymerase: molecular dynamics and docking to understand resistant mutations. Protein Sci 2010; 19: 796–807.
http://www.ncbi.nlm.nih.gov/projects/genotyping/view.cgi?db=2.
Rozanov M, Plikat U, Chappey C, Kochergin A, Tatusova T . A web–based genotyping resource for viral sequences. Nucleic Acids Res 2004; 32: W654–9.
Tuske S, Sarafianos SG, Clark AD, Ding JP, Naeger LK, White KL, et al. Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol 2004; 11: 469–74.
Sali A, Potterton L, Yuan F, van Vlijmen H, Karplus M . Evaluation of comparative protein modeling by MODELLER. Proteins 1995; 23: 318–26.
Laskowski RA, Macarthur MW, Moss DS, Thornton JM . Procheck- a program to check the stereochemical quality of protein structures. J Appl Crystallogr 1993; 26: 283–91.
Schrödinger Suite: Schrödinger, LLC, In. New York; 2008.
Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, et al. The Amber biomolecular simulation programs. J Comput Chem 2005; 26: 1668–88.
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, et al. Gaussian 03, Revision B.05 Gaussian, Inc, Wallingford, CT (2004).
Bayly CI, Cieplak P, Cornell WD, Kollman PA . A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges — the resp model. J Phys Chem-Us 1993; 97: 10269–80.
Wang JM, Wang W, Kollman PA . Antechamber: an accessory software package for molecular mechanical calculations. Abs Pap Am Chem Soc 2001; 222: U403–U03.
Meagher KL, Redman LT, Carlson HA . Development of polyphosphate parameters for use with the AMBER force field. J Comput Chem 2003; 24: 1016–25.
Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed–phase quantum mechanical calculations. J Comput Chem 2003; 24: 1999–2012.
Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA . Development and testing of a general amber force field. J Comput Chem 2004; 25: 1157–74.
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML . Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983; 79: 926–35.
Darden T, York D, Pedersen L . Particle mesh ewald – an N.Log(N) method for ewald sums in large systems. J Chem Phys 1993; 98: 10089–92.
Larini L, Mannella R, Leporini D . Langevin stabilization of molecular–dynamics simulations of polymers by means of quasisymplectic algorithms. J Chem Phys 2007; 126: 104101.
Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000; 33: 889–97.
Weiser J, Shenkin PS, Still WC . Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comput Chem 1999; 20: 217–30.
Yang B, Hamza A, Chen G, Wang Y, Zhan CG . Computational determination of binding structures and free energies of phosphodiesterase-2 with benzo[1,4]diazepin-2-one derivatives. J Phys Chem B 2010; 114: 16020–8.
Wan S, Coveney PV . Molecular dynamics simulation reveals structural and thermodynamic features of kinase activation by cancer mutations within the epidermal growth factor receptor. J Comput Chem 2011; 32: 2843–52.
Gohlke H, Kiel C, Case DA . Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 2003; 330: 891–913.
Venken T, Krnavek D, Munch J, Kirchhoff F, Henklein P, De Maeyer M, et al. An optimized MM/PBSA virtual screening approach applied to an HIV-1 gp41 fusion peptide inhibitor. Proteins 2011; 79: 3221–35.
Onufriev A, Bashford D, Case DA . Exploring protein native states and large–scale conformational changes with a modified generalized born model. Proteins 2004; 55: 383–94.
Massova I, Kollman PA . Computational alanine scanning to probe protein–protein interactions: A novel approach to evaluate binding free energies. J Am Chem Soc 1999; 121: 8133–43.
Stuyver LJ, Locarnini SA, Lok A, Richman DD, Carman WF, Dienstag JL, et al. Nomenclature for antiviral-resistant human hepatitis B virus mutations in the polymerase region. Hepatology 2001; 33: 751–7.
Warner N, Locarnini S, Kuiper M, Bartholomeusz A, Ayres A, Yuen L, et al. The L80I substitution in the reverse transcriptase domain of the hepatitis B virus polymerase is associated with lamivudine resistance and enhanced viral replication in vitro. Antimicrob Agents Chemother 2007; 51: 2285–92.
Liu BM, Li T, Xu J, Li XG, Dong JP, Yan P, et al. Characterization of potential antiviral resistance mutations in hepatitis B virus reverse transcriptase sequences in treatment-naive Chinese patients. Antiviral Res 2010; 85: 512–9.
Li XG, Liu BM, Xu J, Liu XE, Ding H, Li T . Discrepancy of potential antiviral resistance mutation profiles within the HBV reverse transcriptase between nucleos(t)ide analogue-untreated and -treated patients with chronic hepatitis B in a hospital in China. J Med Virol 2012; 84: 207–16.
Acknowledgements
This work is supported by the State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences. The authors gratefully acknowledge financial support from the State Key Program of Basic Research of China (No 2009CB918502), and the National Natural Science Foundation of China (No 81001399).
Author information
Authors and Affiliations
Corresponding authors
Additional information
Supplementary Table and Figure are available at the Acta Pharmacologica Sinica website.
Supplementary information
Supplementary information Table S1
The six standard reference sequences retrieved using NCBI's genotyping tool. (DOC 25 kb)
Supplementary information Table S2
Consensus amino acid reference sequences of HBV polymerase genotype B and C used in the homology modeling. (DOC 19 kb)
Supplementary information Fig. 1
Ramachandran plot of homology model of HBV polymerase genotype B and C. (DOC 154 kb)
Rights and permissions
About this article
Cite this article
Li, J., Du, Y., Liu, X. et al. Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies. Acta Pharmacol Sin 34, 319–328 (2013). https://doi.org/10.1038/aps.2012.146
Received:
Accepted:
Published:
Issue date:
DOI: https://doi.org/10.1038/aps.2012.146
Keywords
This article is cited by
-
Conformation and dynamics of the C-terminal region in human phosphoglycerate mutase 1
Acta Pharmacologica Sinica (2017)
-
Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors
Acta Pharmacologica Sinica (2014)
