Computational model of hepatitis B virus DNA polymerase: Molecular dynamics and docking to understand resistant mutations

Protein Science

Volumn 19, Issue 4, 2010, Pages 796-807

  Daga, Pankaj R ^a   Duan, Jinsong ^a   Doerksen, Robert J ^a,b  

^a UNIVERSITY OF MISSISSIPPI   (United States)

^b UNIVERSITY OF MISSISSIPPI   (United States)

Author keywords

Comparative modeling; Enzyme; Infectious disease; Molecular dynamics; Resistance; Sequence; Triphosphate

Indexed keywords

ANTIVIRUS AGENT; DNA POLYMERASE; DOCKING PROTEIN; HDP INHIBITOR; RNA DIRECTED DNA POLYMERASE INHIBITOR; UNCLASSIFIED DRUG;

ANTIVIRAL RESISTANCE; ARTICLE; BINDING AFFINITY; CONFORMATIONAL TRANSITION; DRUG INACTIVATION; DRUG STRUCTURE; ENZYME BINDING; EXPERIMENTAL MODEL; GENETIC RESISTANCE; HEPATITIS B; HEPATITIS B VIRUS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN STABILITY; STEREOCHEMISTRY; TECHNIQUE; VALIDATION STUDY; VIRUS MUTATION;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; DNA-DIRECTED DNA POLYMERASE; HEPATITIS B VIRUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; VIRAL PROTEINS;

HEPATITIS B VIRUS;

EID: 77950203765     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.359     Document Type: Article

References (35)

1. Lok ASF, Mcmahon BJ (2007) Chronic Hepatitis B. Hepatology 45:507-539.
2. Borgia G, Gentile I (2006) Treating chronic Hepatitis B: today and tomorrow. Curr Med Chem 13:2839-2855.
3. Dienstag J, Easley C, Kirkpatrick P (2007) Telbivudine. Nat Rev Drug Discov 6:267-268.
4. Severini A, Liu XY, Wilson JS, Tyrrell DL (1995) Mechanism of inhibition of duck hepatitis B virus polymerase by (-)- β-L-2′, 3′-dideoxy-3′-thiacytidine. Antimicrob Agents Chemother 39:1430-1435.
5. Deval J, Courcambeck J, Selmi B, Boretto J, Canard B (2004) Structural determinants and molecular mechanisms for the resistance of HIV-1 RT to nucleoside analogues. Curr Durg Metabol 5:305-316.
6. Daga PR, Patel RY, Doerksen RJ (2010) Template-based protein modeling: Recent methodological advances. Curr Top Med Chem 10:84-94.
7. Das K, Xiong X, Yang H, Westland CE, Gibbs CS, Sarafianos SG, Arnold E (2001) Molecular modeling and biochemical characterization reveal the mechanism of Hepatitis B virus polymerase resistance to Lamivudine (3TC) and Emtricitabine (FTC). J Virol 75:4771-4779.
8. Bartholomeusz A, Tehan BG, Chalmers DK (2004) Comparison of the HBV and HIV polymerase, and antiviral resistance mutations. Antiviral Therapy 9:149-160.
9. Langley DR, Walsh AW, Baldick CJ, Eggers BJ, Rose RE, Levine SM, Kapur AJ, Colonno RJ, Tenney DJ (2007) Inhibition of Hepatitis B virus polymerase by Entecavir. J Virol 81:3992-4001.
10. Chong Y, Chu CK (2002) Understanding the unique mechanism of L-FMAU (Clevudine) against Hepatitis B virus: molecular dynamics studies. Bioorg Med Chem Lett 12:3459-3462.
11. Yadav V, Chu CK (2004) Molecular mechanisms of adefovir sensitivity and resistance in HBV polymerase mutants: a molecular dynamics study. Bioorg Med Chem Lett 14:4313-4317.
12. Sharon A, Chu CK (2008) Understanding the molecular basis of HBV drug resistance by molecular modeling. Antiviral Res 80:339-353.
13. Bazmi HZ, Hammond JL, Cavalcanti SCH, Chu CK, Schinazi RF, Mellors JW (2000) In vitro selection of mutations in the human immunodeficiency virus Type 1 reverse transcriptase that decrease susceptibility to (-)-β -D-dioxolane-guanosine and suppress resistance to 3′-azido-3′- deoxythymidine. Antimicrob Agents Chemother 44:1783-1788.
14. Gu Z, Gao Q, Fang H, Salomon H, Parniak MA, Goldberg E, Cameron J, Wainberg MA (1994) Identification of a mutation at codon 65 in the IKKK motif of reverse transcriptase that encodes human immunodeficiency virus resistance to 2′, 3′-dideoxycytidine and 2′, 3′-dideoxy-3′- thiacytidine. Antimicrob Agents Chemother 38:275-281.
15. Gu Z, Salomon H, Cherrington JM, Mulato AS, Chen MS, Yarchoan R, Foli A, Sogocio KM, Wainberg MA (1995) K65R mutation of human immunodeficiency virus type 1 reverse transcriptase encodes cross-resistance to 9-(2- phosphonylmethoxyethyl)adenine. Antimicrob Agents Chemother 39:1888-1891.
16. Tuske S, Sarafianos SG, Clark AD, Ding J, Naeger LK, White KL, Miller MD, Gibbs CS, Boyer PL, Clark P, Wang G, Gaffney BL, Jones RA, Jerina DM, Hughes SH, Arnold E (2004) Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol 11:469-474.
17. Selmi B, Boretto J, Sarfati SR, Guerreiro C, Canard B (2001) Mechanism-based suppression of dideoxynucleotide resistance by K65R human immunodeficiency virus reverse transcriptase using an alpha-boranophosphate nucleoside analogue. J Biol Chem 276:48466-48472.
18. Larder BA, Bloor S, Kemp SD, Hertogs K, Desmet RL, Miller V, Sturmer M, Staszewski S, Ren J, Stammers DK, Pauwels R (1999) A family of insertion mutations between codons 67 and 70 of human immunodeficiency virus type 1 reverse transcriptase confer multinucleoside analog resistance. Antimicrob Agents Chemother 43:1961-1967.
19. Menendez-Arias L, Matamoros T, Cases-Gonzalez CE (2006) Insertions and deletions in HIV-1 reverse transcriptase: consequences for drug resistance and viral fitness. Curr Pharm Des 12:1811-1825.
20. De Clercq E (1999) Perspectives for the treatment of Hepatitis B virus infections. Int J Antimicrob Agents 12:81-95.
21. Ray AS, Basavapathruni A, Anderson KS (2002) Mechanistic studies to understand the progressive development of resistance in human immunodeficiency virus Type 1 reverse transcriptase to Abacavir. J Biol Chem 277:40479-40490.
22. O'Reilly EK, Kao CC (1998) Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure. Virology 252:287-303.
23. Sarafianos SG, Das K, Clark AD, Ding J, Boyer PL, Hughes SH, Arnold E (1999) Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids. Proc Natl Acad Sci USA 96:10027-10032.
24. Chong Y, Stuyver L, Otto MJ, Schinazi RF, Chu CK (2003) Mechanism of antiviral activities of 3′-substituted L-nucleosides against 3TC-resistant HBV polymerase: a molecular modelling approach. Antiviral Chem Chemother 14:309-319.
25. Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170.
26. Dando T, Plosker G (2003) Adefovir dipivoxil: a review of its use in chronic Hepatitis B. Drugs 63:2215-2234.
27. Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, Jones DT (2005) Protein structure prediction servers at University College London. Nucl Acids Res 33: W36-W38.
28. Tripos Associates. SYBYL7.2. (2006) St. Louis, MO: Tripos Associates Inc.
29. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucl Acids Res 22:4673-4680.
30. Huang H, Chopra R, Verdine GL, Harrison SC (1998) Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance. Science 282:1669-1675.
31. Ding J, Das K, Hsiou Y, Sarafianos SG, Clark AD, Jacobo-Molina A, Tantillo C, Hughes SH, Arnold E (1998) Structure and functional implications of the polymerase active site region in a complex of HIV-1 RT with a double-stranded DNA template-primer and an antibody fab fragment at 2.8 A resolution. J Mol Biol 284:1095-1111.
32. Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18:2714-2723.
33. Vullo A, Frasconi P (2004) Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics 20:653-659.
34. 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.
35. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The AMBER biomolecular simulation programs. J Comput Chem 26:1668-1688.