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Items: 1 to 50 of 76

1.

Two Coselected Distal Mutations in HIV-1 Reverse Transcriptase (RT) Alter Susceptibility to Nonnucleoside RT Inhibitors and Nucleoside Analogs.

Boyer PL, Melody K, Smith SJ, Dunn LL, Kline C, Fischer DK, Dwivedi R, Clark P, Hughes SH, Ambrose Z.

J Virol. 2019 May 15;93(11). pii: e00224-19. doi: 10.1128/JVI.00224-19. Print 2019 Jun 1.

2.

Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase.

Boyer PL, Smith SJ, Zhao XZ, Das K, Gruber K, Arnold E, Burke TR Jr, Hughes SH.

J Virol. 2018 Jun 13;92(13). pii: e02203-17. doi: 10.1128/JVI.02203-17. Print 2018 Jul 1.

3.

Analysis of the Zidovudine Resistance Mutations T215Y, M41L, and L210W in HIV-1 Reverse Transcriptase.

Boyer PL, Das K, Arnold E, Hughes SH.

Antimicrob Agents Chemother. 2015 Dec;59(12):7184-96. doi: 10.1128/AAC.05069-14. Epub 2015 Aug 31.

4.

Mutations in human immunodeficiency virus type 1 reverse transcriptase that make it sensitive to degradation by the viral protease in virions are selected against in patients.

Dunn LL, Boyer PL, McWilliams MJ, Smith SJ, Hughes SH.

Virology. 2015 Oct;484:127-35. doi: 10.1016/j.virol.2015.05.020. Epub 2015 Jun 18.

5.

4-amino-1-hydroxy-2-oxo-1,8-naphthyridine-containing compounds having high potency against raltegravir-resistant integrase mutants of HIV-1.

Zhao XZ, Smith SJ, Métifiot M, Marchand C, Boyer PL, Pommier Y, Hughes SH, Burke TR Jr.

J Med Chem. 2014 Jun 26;57(12):5190-202. doi: 10.1021/jm5001908. Epub 2014 Jun 16. Erratum in: J Med Chem. 2014 Aug 14;57(15):6885.

6.

Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles.

Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA.

Chem Biol Drug Des. 2014 May;83(5):521-31. doi: 10.1111/cbdd.12277. Epub 2014 Mar 24.

7.

Mutations in HIV-1 reverse transcriptase cause misfolding and miscleavage by the viral protease.

Dunn LL, Boyer PL, Clark PK, Hughes SH.

Virology. 2013 Sep;444(1-2):241-9. doi: 10.1016/j.virol.2013.06.017. Epub 2013 Jul 11.

8.

HIV-1 and HIV-2 reverse transcriptases: different mechanisms of resistance to nucleoside reverse transcriptase inhibitors.

Boyer PL, Clark PK, Hughes SH.

J Virol. 2012 May;86(10):5885-94. doi: 10.1128/JVI.06597-11. Epub 2012 Mar 21.

9.

4'-C-methyl-2'-deoxyadenosine and 4'-C-ethyl-2'-deoxyadenosine inhibit HIV-1 replication.

Vu BC, Boyer PL, Siddiqui MA, Marquez VE, Hughes SH.

Antimicrob Agents Chemother. 2011 May;55(5):2379-89. doi: 10.1128/AAC.01290-10. Epub 2011 Feb 22.

10.

Foamy retrovirus integrase contains a Pol dimerization domain required for protease activation.

Lee EG, Roy J, Jackson D, Clark P, Boyer PL, Hughes SH, Linial ML.

J Virol. 2011 Feb;85(4):1655-61. doi: 10.1128/JVI.01873-09. Epub 2010 Dec 1.

11.

Structural basis of HIV-1 resistance to AZT by excision.

Tu X, Das K, Han Q, Bauman JD, Clark AD Jr, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E.

Nat Struct Mol Biol. 2010 Oct;17(10):1202-9. doi: 10.1038/nsmb.1908. Epub 2010 Sep 19.

12.

Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.

Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S, Tu X, Clark AD Jr, Boyer PL, Hou X, Gaffney BL, Jones RA, Miller MD, Hughes SH, Arnold E.

J Biol Chem. 2009 Dec 11;284(50):35092-100. doi: 10.1074/jbc.M109.022525. Epub 2009 Oct 7.

13.

The nucleoside analogue D-carba T blocks HIV-1 reverse transcription.

Boyer PL, Vu BC, Ambrose Z, Julias JG, Warnecke S, Liao C, Meier C, Marquez VE, Hughes SH.

J Med Chem. 2009 Sep 10;52(17):5356-64. doi: 10.1021/jm801176e.

14.

Synthesis of conformationally locked carbocyclic nucleoside phosphonates to probe the active site of HIV-1 RT.

Saneyoshi H, Vu BC, Hughes SH, Boyer PL, Sarafianos SG, Marquez VE.

Nucleic Acids Symp Ser (Oxf). 2008;(52):623-4. doi: 10.1093/nass/nrn315.

15.

Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.

Bauman JD, Das K, Ho WC, Baweja M, Himmel DM, Clark AD Jr, Oren DA, Boyer PL, Hughes SH, Shatkin AJ, Arnold E.

Nucleic Acids Res. 2008 Sep;36(15):5083-92. doi: 10.1093/nar/gkn464. Epub 2008 Aug 1.

16.

HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.

Delviks-Frankenberry KA, Nikolenko GN, Boyer PL, Hughes SH, Coffin JM, Jere A, Pathak VK.

Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10943-8. doi: 10.1073/pnas.0804660105. Epub 2008 Jul 30.

17.

D-(+)-iso-methanocarbathymidine: a high-affinity substrate for herpes simplex virus 1 thymidine kinase.

Comin MJ, Vu BC, Boyer PL, Liao C, Hughes SH, Marquez VE.

ChemMedChem. 2008 Jul;3(7):1129-34. doi: 10.1002/cmdc.200800027.

18.

Apparent defects in processive DNA synthesis, strand transfer, and primer elongation of Met-184 mutants of HIV-1 reverse transcriptase derive solely from a dNTP utilization defect.

Gao L, Hanson MN, Balakrishnan M, Boyer PL, Roques BP, Hughes SH, Kim B, Bambara RA.

J Biol Chem. 2008 Apr 4;283(14):9196-205. doi: 10.1074/jbc.M710148200. Epub 2008 Jan 24.

19.

In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT.

Boyer PL, Stenbak CR, Hoberman D, Linial ML, Hughes SH.

Virology. 2007 Oct 25;367(2):253-64. Epub 2007 Jul 12.

20.

The nucleoside analogs 4'C-methyl thymidine and 4'C-ethyl thymidine block DNA synthesis by wild-type HIV-1 RT and excision proficient NRTI resistant RT variants.

Boyer PL, Julias JG, Ambrose Z, Siddiqui MA, Marquez VE, Hughes SH.

J Mol Biol. 2007 Aug 24;371(4):873-82. Epub 2007 May 18.

PMID:
17597154
21.

Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.

Das K, Sarafianos SG, Clark AD Jr, Boyer PL, Hughes SH, Arnold E.

J Mol Biol. 2007 Jan 5;365(1):77-89. Epub 2006 Sep 15.

PMID:
17056061
22.

Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance?

Boyer PL, Sarafianos SG, Clark PK, Arnold E, Hughes SH.

PLoS Pathog. 2006 Feb;2(2):e10. Epub 2006 Feb 17.

24.

Fixed conformation nucleoside analogs effectively inhibit excision-proficient HIV-1 reverse transcriptases.

Boyer PL, Julias JG, Marquez VE, Hughes SH.

J Mol Biol. 2005 Jan 21;345(3):441-50.

PMID:
15581889
25.

A 4'-C-ethynyl-2',3'-dideoxynucleoside analogue highlights the role of the 3'-OH in anti-HIV active 4'-C-ethynyl-2'-deoxy nucleosides.

Siddiqui MA, Hughes SH, Boyer PL, Mitsuya H, Van QN, George C, Sarafinanos SG, Marquez VE.

J Med Chem. 2004 Oct 7;47(21):5041-8.

PMID:
15456247
26.
27.

Characterization of the polymerase and RNase H activities of human foamy virus reverse transcriptase.

Boyer PL, Stenbak CR, Clark PK, Linial ML, Hughes SH.

J Virol. 2004 Jun;78(12):6112-21.

28.

Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants.

Das K, Clark AD Jr, Lewi PJ, Heeres J, De Jonge MR, Koymans LM, Vinkers HM, Daeyaert F, Ludovici DW, Kukla MJ, De Corte B, Kavash RW, Ho CY, Ye H, Lichtenstein MA, Andries K, Pauwels R, De Béthune MP, Boyer PL, Clark P, Hughes SH, Janssen PA, Arnold E.

J Med Chem. 2004 May 6;47(10):2550-60.

PMID:
15115397
29.

Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir.

Tuske S, Sarafianos SG, Clark AD Jr, 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.

Nat Struct Mol Biol. 2004 May;11(5):469-74. Epub 2004 Apr 25.

PMID:
15107837
30.

Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis.

Julias JG, Boyer PL, McWilliams MJ, Alvord WG, Hughes SH.

Virology. 2004 Apr 25;322(1):13-21.

31.

PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1.

Sismour AM, Lutz S, Park JH, Lutz MJ, Boyer PL, Hughes SH, Benner SA.

Nucleic Acids Res. 2004 Feb 2;32(2):728-35. Print 2004.

32.

On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data.

Lewi PJ, de Jonge M, Daeyaert F, Koymans L, Vinkers M, Heeres J, Janssen PA, Arnold E, Das K, Clark AD Jr, Hughes SH, Boyer PL, de Béthune MP, Pauwels R, Andries K, Kukla M, Ludovici D, De Corte B, Kavash R, Ho C.

J Comput Aided Mol Des. 2003 Feb-Apr;17(2-4):129-34. Erratum in: J Comput Aided Mol Des. 2003 May-Jun;17(5-6):398. Lewis PJ [corrected to Lewi PJ].

PMID:
13677481
33.

A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude.

Choi Y, George C, Comin MJ, Barchi JJ Jr, Kim HS, Jacobson KA, Balzarini J, Mitsuya H, Boyer PL, Hughes SH, Marquez VE.

J Med Chem. 2003 Jul 17;46(15):3292-9.

PMID:
12852759
34.

A novel mechanism for inhibition of HIV-1 reverse transcriptase.

Skillman AG, Maurer KW, Roe DC, Stauber MJ, Eargle D, Ewing TJ, Muscate A, Davioud-Charvet E, Medaglia MV, Fisher RJ, Arnold E, Gao HQ, Buckheit R, Boyer PL, Hughes SH, Kuntz ID, Kenyon GL.

Bioorg Chem. 2002 Dec;30(6):443-58.

PMID:
12642128
35.

Trapping HIV-1 reverse transcriptase before and after translocation on DNA.

Sarafianos SG, Clark AD Jr, Tuske S, Squire CJ, Das K, Sheng D, Ilankumaran P, Ramesha AR, Kroth H, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E.

J Biol Chem. 2003 May 2;278(18):16280-8. Epub 2003 Jan 28.

36.

Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.

Sarafianos SG, Clark AD Jr, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E.

EMBO J. 2002 Dec 2;21(23):6614-24.

38.

Mutation of the catalytic domain of the foamy virus reverse transcriptase leads to loss of processivity and infectivity.

Rinke CS, Boyer PL, Sullivan MD, Hughes SH, Linial ML.

J Virol. 2002 Aug;76(15):7560-70.

40.

Cross-linking of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase to template-primer.

Peletskaya EN, Boyer PL, Kogon AA, Clark P, Kroth H, Sayer JM, Jerina DM, Hughes SH.

J Virol. 2001 Oct;75(19):9435-45.

42.
43.

The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.

Hsiou Y, Ding J, Das K, Clark AD Jr, Boyer PL, Lewi P, Janssen PA, Kleim JP, Rösner M, Hughes SH, Arnold E.

J Mol Biol. 2001 Jun 1;309(2):437-45.

PMID:
11371163
44.

Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase.

Boyer PL, Sarafianos SG, Arnold E, Hughes SH.

J Virol. 2001 May;75(10):4832-42.

45.

The basic loop of the RNase H domain of MLV RT is important both for RNase H and for polymerase activity.

Boyer PL, Gao HQ, Frank P, Clark PK, Hughes SH.

Virology. 2001 Mar 30;282(1):206-13.

46.

Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.

Sarafianos SG, Das K, Tantillo C, Clark AD Jr, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E.

EMBO J. 2001 Mar 15;20(6):1449-61.

47.

The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase.

Gao HQ, Boyer PL, Sarafianos SG, Arnold E, Hughes SH.

J Mol Biol. 2000 Jul 7;300(2):403-18.

PMID:
10873473
49.

Analysis of mutations at positions 115 and 116 in the dNTP binding site of HIV-1 reverse transcriptase.

Boyer PL, Sarafianos SG, Arnold E, Hughes SH.

Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3056-61.

50.

Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids.

Sarafianos SG, Das K, Clark AD Jr, Ding J, Boyer PL, Hughes SH, Arnold E.

Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10027-32.

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