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Our Science – Hughes Website

Stephen H. Hughes, Ph.D.

Selected Publications

1)  Zhao XZ, Smith SJ, Métifiot M, Johnson BC, Marchand C, Pommier Y, Hughes SH, Burke TR.
Bicyclic 1-Hydroxy-2-oxo-1,2-dihydropyridine-3-carboxamide-Containing HIV-1 Integrase Inhibitors Having High Antiviral Potency against Cells Harboring Raltegravir-Resistant Integrase Mutants.
J. Med. Chem. 57: 1573-82, 2014.
2)  De Ravin SS, Su L, Theobald N, Choi U, Macpherson JL, Poidinger M, Symonds G, Pond SM, Ferris AL, Hughes SH, Malech HL, Wu X.
Enhancers are major targets for murine leukemia virus vector integration.
J. Virol. 88: 4504-13, 2014.
3)  Varadarajan J, McWilliams M, Hughes S.
Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations.
Proc Natl Acad Sci U S A. 110: 14747-14752, 2013.
Full Text Article. [Journal]
4)  Dunn LL, Boyer PL, Clark PK, Hughes SH.
Mutations in HIV-1 reverse transcriptase cause misfolding and miscleavage by the viral protease.
Virology. 444: 241-249, 2013.
Full Text Article. [Journal]
5)  Johnson B, Metifiot M, Ferris A, Pommier Y, Hughes S.
A homology model of HIV-1 integrase and analysis of mutations designed to test the model.
J Mol Biol. 425: 2133-2146, 2013.
Full Text Article. [Journal]
6)  Lauberth SM, Nakayama T, Wu X, Ferris AL, Tang Z, Hughes SH, Roeder RG.
H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation.
Cell. 152: 1021-36, 2013.
7)  Johnson BC, Pauly GT, Rai G, Patel D, Bauman JD, Baker HL, Das K, Schneider JP, Maloney DJ, Arnold E, Thomas CJ, Hughes SH.
A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants.
Retrovirology. 9: 99, 2012.
Full Text Article. [Journal]
8)  De Ravin SS, Gray JT, Throm RE, Spindler J, Kearney M, Wu X, Coffin JM, Hughes SH, Malderelli F, Sorrentino BP, Malech HL.
False-Positive HIV PCR Test Following Ex Vivo Lentiviral Gene Transfer Treatment of X-linked Severe Combined Immunodeficiency Vector.
Mol. Ther. 22: 244-5, 2014.
9)  Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JA, Hughes SH, McCammon JA.
Discovery of Novel Inhibitors of HIV-1 Reverse Transcriptase Through Virtual Screening of Experimental and Theoretical Ensembles.
Chem Biol Drug Des. 2014.
10)  Smith S, Hughes S.
Rapid screening of HIV reverse transcriptase and integrase inhibitors.
J Vis Exp. 2014.
In Press. [Journal]
11)  Das K, Arnold E, Hughes S.
Lennarz W, Lane M, eds.
HIV-1 reverse transcriptase structures. In: Encyclopedia of Biological Chemistry.
.: Elsevier; 2013. p. 548-553 [Book Chapter]
12)  Metifiot M, Maddali K, Johnson BC, Hare S, Smith SJ, Zhao XZ, Marchand C, Burke TR, Hughes SH, Cherepanov P, Pommier Y.
Activities, crystal structures, and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase.
ACS Chem. Biol. 8: 209-17, 2013.
13)  Koh Y, Wu X, Ferris AL, Matreyek KA, Smith SJ, Lee K, Kewalramani VN, Hughes SH, Engelman A.
Differential Effects of Human Immunodeficiency Virus Type 1 Capsid and Cellular Factors Nucleoporin 153 and LEDGF/p75 on the Efficiency and Specificity of Viral DNA Integration.
J. Virol. 87: 648-58, 2013.
14)  Kirby KA, Michailidis E, Fetterly TL, Steinbach MA, Singh K, Marchand B, Leslie MD, Hagedorn AN, Kodama EN, Marquez VE, Hughes SH, Mitsuya H, Parniak MA, Sarafianos SG.
Effects of substitutions at the 4" and 2 positions on the bioactivity of 4"-ethynyl-2-fluoro-2"-deoxyadenosine.
Antimicrob. Agents Chemother. 57: 6254-64, 2013.
15)  Li Y, Ferris A, Lewis B, Orsulic S, Williams B, Holland E, Hughes S.
The RCAS/TVA somatic gene transfer method in modeling human cancer. In: Genetically Engineered Mice for Cancer Research: Design, Analysis, Pathways, Validation and Pre-clinical Testing (Green, J.E., and Ried, T., eds,).
-: Springer Publications; 2012. p. 83-112 [Book Chapter]
16)  Zhao XZ, Maddali K, Smith SJ, Métifiot M, Johnson BC, Marchand C, Hughes SH, Pommier Y, Burke TR.
6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 integrase inhibitors.
Bioorg. Med. Chem. Lett. 2012.
17)  Zhao XZ, Maddali K, Metifiot M, Smith SJ, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR.
Bicyclic Hydroxy-1H-pyrrolopyridine-trione Containing HIV-1 Integrase Inhibitors.
Chem Biol Drug Des. 79: 157-165, 2012.
18)  Boyer PL, Clark PK, Hughes SH.
HIV-1 and HIV-2 Reverse Transcriptases: Different Mechanisms of Resistance to Nucleoside Reverse Transcriptase Inhibitors.
J. Virol. 86: 5885-94, 2012.
19)  Hu WS, Hughes SH.
HIV-1 Reverse Transcription.
Cold Spring Harb Perspect Med. 2, 2012.
20)  Wang H, Jurado KA, Wu X, Shun MC, Li X, Ferris AL, Smith SJ, Patel PA, Fuchs JR, Cherepanov P, Kvaratskhelia M, Hughes SH, Engelman A.
HRP2 determines the efficiency and specificity of HIV-1 integration in LEDGF/p75 knockout cells but does not contribute to the antiviral activity of a potent LEDGF/p75-binding site integrase inhibitor.
Nucleic Acids Res. 40: 11518-11530, 2012.
21)  Ambrose Z, Lee K, Ndjomou J, Xu H, Oztop I, Matous J, Takemura T, Unutmaz D, Engelman A, Hughes SH, Kewalramani VN.
Human Immunodeficiency Virus Type 1 Capsid Mutation N74D Alters Cyclophilin A Dependence and Impairs Macrophage Infection.
J. Virol. 86: 4708-14, 2012.
22)  Elleder D, Baiga TJ, Russell RL, Naughton JA, Hughes SH, Noel JP, Young JA.
Identification of a 3-Aminoimidazo[1,2-a]Pyridine Inhibitor of HIV-1 Reverse Transcriptase.
Virol. J. 9: 305, 2012.
23)  Johnson BC, Métifiot M, Pommier Y, Hughes SH.
Molecular Dynamics Approaches Estimate the Binding Energy of HIV-1 Integrase Inhibitors and Correlate with In Vitro Activity.
Antimicrob. Agents Chemother. 56: 411-9, 2012.
24)  Kearney M, Spindler J, Wiegand A, Shao W, Anderson E, Maldarelli F, Ruscetti F, Mellors J, Hughes S, Le Grice S, Coffin J.
Multiple sources of contamination in samples from patients reported to have XMRV infection.
PLoS ONE. 7(2): e30889, 2012.
Full Text Article. [Journal]
25)  Chung S, Miller JT, Johnson BC, Hughes SH, Le Grice SF.
Mutagenesis of human immunodeficiency virus reverse transcriptase p51 subunit defines residues contributing to vinylogous urea inhibition of ribonuclease H activity.
J Biol Chem. 287: 4066-4075, 2012.
Full Text Article. [Journal]
26)  Vu BC, Boyer PL, Siddiqui MA, Marquez VE, Hughes SH.
4'-C-Methyl-2'-Deoxyadenosine and 4'-C-Ethyl-2'-Deoxyadenosine Inhibit HIV-1 Replication.
Antimicrob. Agents Chemother. 55: 2379-89, 2011.
27)  Zhao XZ, Maddali K, Metifiot M, Smith SJ, Vu BC, Marchand C, Hughes SH, Pommier Y, Burke TR.
Development of tricyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors.
Bioorg. Med. Chem. Lett. 21: 2986-90, 2011.
28)  Lee E, Roy J, Jackson D, Clark P, Boyer PL, Hughes SH, Linial ML.
Foamy retroviral integrase contains a Pol dimerization domain required for protease activation.
J Virol. 85: 1655-1661, 2011.
Full Text Article. [Journal]
29)  Métifiot M, Johnson B, Smith S, Zhao XZ, Marchand C, Burke T, Hughes S, Pommier Y.
MK-0536 inhibits HIV-1 integrases resistant to raltegravir.
Antimicrob. Agents Chemother. 55: 5127-33, 2011.
30)  Kaczmarczyk SJ, Sitaraman K, Young HA, Hughes SH, Chatterjee DK.
Protein delivery using engineered virus-like particles.
Proc. Natl. Acad. Sci. U.S.A. 108: 16998-7003, 2011.
31)  Hare S, Smith SJ, Métifiot M, Jaxa-Chamiec A, Pommier Y, Hughes SH, Cherepanov P.
Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572).
Mol. Pharmacol. 80: 565-72, 2011.
32)  Davis CA, Parniak MA, Hughes SH.
The effects of RNase H inhibitors and nevirapine on the susceptibility of HIV-1 to AZT and 3TC.
Virology. 419: 64-71, 2011.
33)  Lee K, Ambrose Z, Martin TD, Oztop I, Mulky A, Julias JG, Vandegraaff N, Baumann JG, Wang R, Yuen W, Takemura T, Shelton K, Taniuchi I, Li Y, Sodroski J, Littman DR, Coffin JM, Hughes SH, Unutmaz D, Engelman A, Kewalramani VN.
Flexible Use of Nuclear Import Pathways by HIV-1.
Cell Host Microbe. 7: 221-233, 2010.
34)  Ferris AL, Wu X, Hughes CM, Stewart C, Smith SJ, Milne TA, Wang GG, Shun MC, Allis CD, Engelman A, Hughes SH.
Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration.
Proc. Natl. Acad. Sci. U.S.A. 107: 3135-40, 2010.
35)  Abram ME, Ferris AL, Shao W, Alvord WG, Hughes SH.
Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication.
J. Virol. 84: 9864-78, 2010.
36)  Tu X, Das K, Han Q, Bauman JD, Clark AD, Hou X, Frenkel YV, Gaffney BL, Jones RA, Boyer PL, Hughes SH, Sarafianos SG, Arnold E.
Structural basis of HIV-1 resistance to AZT by excision.
Nat. Struct. Mol. Biol. 17: 1202-1209, 2010.
37)  Sheng-Fowler L, Cai F, Fu H, Zhu Y, Orrison B, Foseh G, Blair DG, Hughes SH, Coffin JM, Lewis AM, Peden K.
Tumors induced in mice by direct inoculation of plasmid DNA expressing both activated H-ras and c-myc.
Int. J. Biol. Sci. 6: 151-62, 2010.
38)  Zhao XZ, Maddali K, Christie Vu B, Marchand C, Hughes SH, Pommier Y, Burke TR.
Examination of halogen substituent effects on HIV-1 integrase inhibitors derived from 2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-ones and 4,5-dihydroxy-1H-isoindole-1,3(2H)-diones.
Bioorg. Med. Chem. Lett. 19: 2714-2717, 2009.
39)  Dunn LL, McWilliams MJ, Das K, Arnold E, Hughes SH.
Mutations in the thumb allow human immunodeficiency virus type 1 reverse transcriptase to be cleaved by protease in virions.
J. Virol. 83: 12336-44, 2009.
40)  Russ PL, Gonzalez-Moa MJ, Vu BC, Sigano DM, Kelley JA, Lai CC, Deschamps JR, Hughes SH, Marquez VE.
North- and South-Bicyclo[3.1.0]Hexene Nucleosides: The Effect of Ring Planarity on Anti-HIV Activity.
ChemMedChem. 4: 1354-1363, 2009.
41)  Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S, Tu X, Clark AD, Boyer PL, Hou X, Gaffney BL, Jones RA, Miller MD, Hughes SH, Arnold E.
Structural basis for the role of the K65r mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance.
J. Biol. Chem. 284: 35092-100, 2009.
42)  Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E.
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition.
J. Mol. Biol. 385: 693-713, 2009.
43)  Himmel DM, Maegley KA, Pauly TA, Bauman JD, Das K, Dharia C, Clark AD, Ryan K, Hickey MJ, Love RA, Hughes SH, Bergqvist S, Arnold E.
Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site.
Structure. 17: 1625-35, 2009.
44)  Boyer PL, Vu BC, Ambrose Z, Julias JG, Warnecke S, Liao C, Meier C, Marquez VE, Hughes SH.
The nucleoside analogue D-carba T blocks HIV-1 reverse transcription.
J. Med. Chem. 52: 5356-64, 2009.
45)  Bauman JD, Das K, Ho WC, Baweja M, Himmel DM, Clark AD, Oren DA, Boyer PL, Hughes SH, Shatkin AJ, Arnold E.
Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
Nucleic Acids Res. 36: 5083-92, 2008.
46)  Delviks-Frankenberry KA, Nikolenko GN, Boyer PL, Hughes SH, Coffin JM, Jere A, Pathak VK.
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision.
Proc. Natl. Acad. Sci. U.S.A. 105: 10943-10948, 2008.
47)  Oh J, Chang KW, Hughes SH.
Integration of Rous sarcoma virus DNA: A CA dinucleotide is not required for the integration of the U3 end of viral DNA.
J. Virol. 2008.
48)  Hu J, Renaud G, Golmes T, Ferris A, Hendrie PC, Donahue RE, Hughes SH, Wolfsberg TG, Russell DW, Dunbar CE.
Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors.
Mol. Ther. 16: 1617-23, 2008.
49)  Saneyoshi H, Vu BC, Hughes SH, Boyer PL, Sarafianos SG, Marquez VE.
Synthesis of conformationally locked carbocyclic nucleoside phosphonates to probe the active site of HIV-1 RT.
Nucleic Acids Symp Ser (Oxf). 623-4, 2008.
50)  Zhao XZ, Semenova EA, Vu BC, Maddali K, Marchand C, Hughes SH, Pommier Y, Burke TR.
2,3-Dihydro-6,7-dihydroxy-1H-isoindol-1-one-Based HIV-1 Integrase Inhibitors.
J Med Chem. 51: 251-259, 2008.
51)  Gao L, Hanson MN, Balakrishnan M, Boyer PL, Roques BP, Hughes SH, Kim B, Bambara RA.
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.
J. Biol. Chem. 283: 9196-205, 2008.
52)  Comin MJ, Vu BC, Boyer PL, Liao C, Hughes SH, Marquez VE.
D-(+)-iso-Methanocarbathymidine: a High-Affinity Substrate for Herpes Simplex Virus 1 Thymidine Kinase.
ChemMedChem. 3: 1129-1134, 2008.
53)  Das K, Bauman JD, Clark AD, Frenkel YV, Lewi PJ, Shatkin AJ, Hughes SH, Arnold E.
High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations.
Proc. Natl. Acad. Sci. U.S.A. 105: 1466-71, 2008.
54)  McWilliams MJ, Julias JG, Hughes SH.
Mutations in the human immunodeficiency virus type 1 polypurine tract (PPT) reduce the rate of PPT cleavage and plus-strand DNA synthesis.
J. Virol. 82: 5104-8, 2008.
55)  Oh J, McWilliams MJ, Julias JG, Hughes SH.
Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo.
J. Virol. 82: 719-27, 2008.
56)  Sheng L, Cai F, Zhu Y, Pal A, Athanasiou M, Orrison B, Blair DG, Hughes SH, Coffin JM, Lewis AM, Peden K.
Oncogenicity of DNA in vivo: Tumor induction with expression plasmids for activated H-ras and c-myc.
Biologicals. 36: 184-97, 2008.
57)  Oh J, Chang KW, Wierzchoslawski R, Alvord WG, Hughes SH.
Rous sarcoma virus (RSV) integration in vivo: a CA dinucleotide is not required in U3, and RSV linear DNA does not autointegrate.
J. Virol. 82: 503-12, 2008.
58)  Chang KW, Oh J, Alvord WG, Hughes SH.
The effects of alternate polypurine tracts (PPTs) and mutations of sequences adjacent to the PPT on viral replication and cleavage specificity of the Rous sarcoma virus reverse transcriptase.
J. Virol. 82: 8592-604, 2008.
59)  Hughes S, Crise B.
Using viral vectors in animal research. In: Anthology of Biosafety (Richmond, JY, ed). Volume X, Animal Biosafety.
.: American Biological Safety Association; 2007. p. 145-166 [Book Chapter]
60)  Mulky A, Vu BC, Conway JA, Hughes SH, Kappes JC.
Analysis of amino acids in the beta7-beta8 loop of human immunodeficiency virus type 1 reverse transcriptase for their role in virus replication.
J. Mol. Biol. 365: 1368-78, 2007.
61)  Das K, Sarafianos SG, Clark AD, Boyer PL, Hughes SH, Arnold E.
Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097.
J. Mol. Biol. 365: 77-89, 2007.
62)  Derse D, Crise B, Li Y, Princler G, Lum N, Stewart C, McGrath CF, Hughes SH, Munroe DJ, Wu X.
Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses.
J. Virol. 81: 6731-41, 2007.
63)  Jones FD, Hughes SH.
In vitro analysis of the effects of mutations in the G-tract of the human immunodeficiency virus type 1 polypurine tract on RNase H cleavage specificity.
Virology. 360: 341-9, 2007.
64)  Boyer PL, Stenbak CR, Hoberman D, Linial ML, Hughes SH.
In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT.
Virology. 367: 253-64, 2007.
65)  Morningstar ML, Roth T, Farnsworth DW, Smith MK, Watson K, Buckheit RW, Das K, Zhang W, Arnold E, Julias JG, Hughes SH, Michejda CJ.
Synthesis, Biological Activity, and Crystal Structure of Potent Nonnucleoside Inhibitors of HIV-1 Reverse Transcriptase That Retain Activity against Mutant Forms of the Enzyme.
J Med Chem. 50: 4003-4015, 2007.
66)  Wu CK, Gousset K, Hughes SH.
Targeting to the endoplasmic reticulum improves the folding of recombinant human telomerase reverse transcriptase.
Protein Expr. Purif. 56: 8-19, 2007.
67)  Boyer PL, Julias JG, Ambrose Z, Siddiqui MA, Marquez VE, Hughes SH.
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.
J. Mol. Biol. 371: 873-82, 2007.
68)  Hu J, Ferris A, Larochelle A, Krouse AE, Metzger ME, Donahue RE, Hughes SH, Dunbar CE.
Transduction of rhesus macaque hematopoietic stem and progenitor cells with avian sarcoma and leukosis virus vectors.
Hum. Gene Ther. 18: 691-700, 2007.
69)  Oh J, Chang K, Alvord G, Hughes S.
Alternate polypurine tracts affect Rous sarcoma virus integration in vivo.
J Virol. 80: 10281-10284, 2006.
Full Text Article. [Journal]
70)  McWilliams MJ, Julias JG, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.
Combining mutations in HIV-1 reverse transcriptase with mutations in the HIV-1 polypurine tract affects RNase H cleavages involved in PPT utilization.
Virology. 348: 378-88, 2006.
71)  Himmel DM, Sarafianos SG, Dharmasena S, Hossain MM, McCoy-Simandle K, Ilina T, Clark AD, Knight JL, Julias JG, Clark PK, Krogh-Jespersen K, Levy RM, Hughes SH, Parniak MA, Arnold E.
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
ACS Chem. Biol. 1: 702-12, 2006.
72)  Oh J, Chang KW, Hughes SH.
Mutations in the U5 Sequences Adjacent to the Primer Binding Site Do Not Affect tRNA Cleavage by Rous Sarcoma Virus RNase H but Do Cause Aberrant Integrations In Vivo.
J Virol. 80: 451-9, 2006.
73)  Garfinkel DJ, Stefanisko KM, Nyswaner KM, Moore SP, Oh J, Hughes SH.
Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap.
J. Virol. 80: 11920-34, 2006.
74)  Marquez VE, Hughes SH, Sei S, Agbaria R.
The history of N-methanocarbathymidine: The investigation of a conformational concept leads to the discovery of a potent and selective nucleoside antiviral agent.
Antiviral Res. 71: 268-75, 2006.
75)  Ambrose Z, Julias JG, Boyer PL, Kewalramani VN, Hughes SH.
The Level of Reverse Transcriptase (RT) in Human Immunodeficiency Virus Type 1 Particles Affects Susceptibility to Nonnucleoside RT Inhibitors but Not to Lamivudine.
J Virol. 80: 2578-81, 2006.
76)  Boyer PL, Sarafianos SG, Clark PK, Arnold E, Hughes SH.
Why Do HIV-1 and HIV-2 Use Different Pathways to Develop AZT Resistance?.
PLoS Pathog. 2: e10, 2006.
77)  Janssen PA, Lewi PJ, Arnold E, Daeyaert F, de Jonge M, Heeres J, Koymans L, Vinkers M, Guillemont J, Pasquier E, Kukla M, Ludovici D, Andries K, de Béthune MP, Pauwels R, Das K, Clark AD, Frenkel YV, Hughes SH, Medaer B, De Knaep F, Bohets H, De Clerck F, Lampo A, Williams P, Stoffels P.
In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine).
J Med Chem. 48: 1901-9, 2005.
78)  Chang KW, Julias JG, Alvord WG, Oh J, Hughes SH.
Alternate polypurine tracts (PPTs) affect the rous sarcoma virus RNase H cleavage specificity and reveal a preferential cleavage following a GA dinucleotide sequence at the PPT-U3 junction.
J Virol. 79: 13694-704, 2005.
79)  Himmel DM, Das K, Clark AD, Hughes SH, Benjahad A, Oumouch S, Guillemont J, Coupa S, Poncelet A, Csoka I, Meyer C, Andries K, Nguyen CH, Grierson DS, Arnold E.
Crystal Structures for HIV-1 Reverse Transcriptase in Complexes with Three Pyridinone Derivatives: A New Class of Non-Nucleoside Inhibitors Effective against a Broad Range of Drug-Resistant Strains.
J Med Chem. 48: 7582-7591, 2005.
80)  Das K, Lewi PJ, Hughes SH, Arnold E.
Crystallography and the design of anti-AIDS drugs: Conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors.
Prog Biophys Mol Biol. 88: 209-31, 2005.
81)  Boyer PL, Julias JG, Marquez VE, Hughes SH.
Fixed conformation nucleoside analogs effectively inhibit excision-proficient HIV-1 reverse transcriptases.
J Mol Biol. 345: 441-50, 2005.
82)  Chang KW, Barsov EV, Ferris AL, Hughes SH.
Mutations of a residue within the polypurine-rich region of Env alter the replication rate and level of cytopathic effects in chimeric avian retroviral vectors.
J Virol. 79: 10258-67, 2005.
83)  Hughes SH.
Wiggling and jiggling can increase the effectiveness of AIDS drugs.
Frontiers Sci. 4: 7-8, 2005.
84)  Siddiqui MA, Hughes SH, Boyer PL, Mitsuya H, Van QN, George C, Sarafinanos SG, Marquez VE.
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.
J Med Chem. 47: 5041-8, 2004.
85)  Boyer PL, Stenbak CR, Clark PK, Linial ML, Hughes SH.
Characterization of the polymerase and RNase H activities of human foamy virus reverse transcriptase.
J Virol. 78: 6112-6121, 2004.
86)  Sarafianos SG, Hughes SH, Arnold E.
Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugs.
Int J Biochem Cell Biol. 36: 1706-15, 2004.
87)  Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.
Effects of mutations in the G-tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage.
J Virol. 78: 13315-24, 2004.
88)  Boyer PL, Imamichi T, Sarafianos SG, Arnold E, Hughes SH.
Effects of the delta 67 complex of mutations in human immunodeficiency virus type 1 reverse transcriptase on nucleoside analog excision.
J Virol. 78: 9987-97, 2004.
89)  Kvaratskhelia M, Clark PK, Hess S, Melder DC, Federspiel MJ, Hughes SH.
Identification of glycosylation sites in the SU component of the Avian Sarcoma/Leukosis virus Envelope Glycoprotein (Subgroup A) by mass spectrometry.
Virology. 326: 171-81, 2004.
90)  Ambrose Z, Boltz V, Palmer S, Coffin JM, Hughes SH, Kewalramani VN.
In vitro characterization of a simian immunodeficiency virus-human immunodeficiency virus (HIV) chimera expressing HIV type 1 reverse transcriptase to study antiviral resistance in pigtail macaques.
J Virol. 78: 13553-61, 2004.
91)  Julias JG, Boyer PL, McWilliams MJ, Alvord WG, Hughes SH.
Mutations at position 184 of human immunodeficiency virus type1 reverse transcriptase affect virus titer and viral DNA synthesis.
Virology. 322: 13-21, 2004.
92)  Peletskaya EN, Kogon AA, Tuske S, Arnold E, Hughes SH.
Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA.
J Virol. 78: 3387-3397, 2004.
93)  Sismour AM, Lutz S, Park JH, Lutz MJ, Boyer PL, Hughes SH, Benner SA.
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1.
Nucleic Acids Res. 32: 728-35, 2004.
94)  Das K, Clark AD, 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.
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.
J Med Chem. 47: 2550-60, 2004.
95)  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.
Structures of HIV-1 RT/DNA complexes before and after incorporation of tenofovir, a nucleotide anti-AIDS drug.
Nat Struct Mol Biol. 11: 469-74, 2004.
96)  Sarafianos SG, Das K, Hughes SH, Arnold E.
Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases.
Curr Opin Struct Biol. 14: 716-30, 2004.
97)  Hughes SH.
The RCAS vector system.
Folia Biol (Praha). 50: 107-19, 2004.
98)  Choi Y, George C, Comin MJ, Barchi JJ, Kim HS, Jacobson KA, Balzarini J, Mitsuya H, Boyer PL, Hughes SH, Marquez VE.
A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude.
J Med Chem. 46: 3292-3299, 2003.
99)  Kroeger-Smith MB, Ruby S, Horouzhenko S, Buckingham B, Richardson J, Puleri I, Potts E, Jorgensen WL, Arnold E, Zhang W, Hughes SH, Michejda CJ, Smith Jr RH.
HIV-1 reverse transcriptase variants: Molecular modeling of Y181C, V106A, L100I, and K103N mutations with nonnucleoside inhibitors using Monte Carlo simulations in combination with a linear response method.
Drug Des Discov. 18: 151-163, 2003.
100)  Julias JG, McWilliams MJ, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.
Mutation of amino acids in the connection domain of human immunodeficiency virus type 1 reverse transcriptase that contact the template-primer affects RNase H activity.
J Virol. 77: 8548-54, 2003.
101)  McWilliams MJ, Julias JG, Sarafianos SG, Alvord WG, Arnold E, Hughes SH.
Mutations in the 5' end of the human immunodeficiency virus type 1 polypurine tract affect RNase H cleavage specificity and virus titer.
J Virol. 77: 11150-7, 2003.
102)  Lewi PJ, de Jonge M, Daeyaert F, Koymans L, Vinkers M, Heeres J, Janssen PA, Arnold E, Das K, Clark AD, Hughes SH, Boyer PL, de Béthune MP, Pauwels R, Andries K, Kukla M, Ludovici D, De Corte B, Kavash R, Ho C, Lewis PJ.
On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data.
J Comput Aided Mol Des. 17: 129-34, 2003.
103)  Princler GL, Julias JG, Hughes SH, Derse D.
Roles of viral and cellular proteins in the expression of alternatively spliced HTLV-1 pX mRNAs.
Virology. 317: 136-45, 2003.
104)  Golinelli MP, Hughes SH.
Secondary structure in the nucleic acid affects the rate of HIV-1 nucleocapsid-mediated strand annealing.
Biochemistry. 42: 8153-62, 2003.
105)  Sarafianos SG, Clark AD, Tuske S, Squire CJ, Das K, Sheng D, Ilankumaran P, Ramesha AR, Kroth H, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E.
Trapping HIV-1 reverse transcriptase before and after translocation on DNA.
J Biol Chem. 278: 16280-8, 2003.
106)  Kroeger Smith MB, Hose BM, Hawkins A, Lipchock J, Farnsworth DW, Rizzo RC, Tirado-Rives J, Arnold E, Zhang W, Hughes SH, Jorgensen WL, Michejda CJ, Smith RH.
Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues.
J Med Chem. 46: 1940-7, 2003.
107)  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.
A novel mechanism for inhibition of HIV-1 reverse transcriptase.
Bioorg Chem. 30: 443-58, 2002.
108)  Rausch JW, Lener D, Miller JT, Julias JG, Hughes SH, Le Grice SF.
Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity.
Biochemistry. 41: 4856-65, 2002.
109)  Tam W, Hughes SH, Hayward WS, Besmer P.
Avian bic, a gene isolated from a common retroviral site in avian leukosis virus-induced lymphomas that encodes a noncoding RNA, cooperates with c-myc in lymphomagenesis and erythroleukemogenesis.
J Virol. 76: 4275-86, 2002.
110)  Oh J, Julias JG, Ferris AL, Hughes SH.
Construction and characterization of a replication-competent retroviral shuttle vector plasmid.
J Virol. 76: 1762-8, 2002.
111)  Rinke CS, Boyer PL, Sullivan MD, Hughes SH, Linial ML.
Mutation of the catalytic domain of the foamy virus reverse transcriptase leads to loss of processivity and infectivity.
J Virol. 76: 7560-70, 2002.
112)  Julias JG, McWilliams MJ, Sarafianos SG, Arnold E, Hughes SH.
Mutations in the RNase H domain of HIV-1 reverse transcriptase affect the initiation of DNA synthesis and the specificity of RNase H cleavage in vivo.
Proc Natl Acad Sci U S A. 99: 9515-20, 2002.
113)  Golinelli MP, Hughes SH.
Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro.
Virology. 294: 122-34, 2002.
114)  Golinelli MP, Hughes SH.
Nontemplated nucleotide addition by HIV-1 reverse transcriptase.
Biochemistry. 41: 5894-906, 2002.
115)  Boyer PL, Sarafianos SG, Arnold E, Hughes SH.
Nucleoside analog resistance caused by insertions in the fingers of human immunodeficiency virus type 1 reverse transcriptase involves ATP-mediated excision.
J Virol. 76: 9143-51, 2002.
116)  Sarafianos SG, Clark AD, Das K, Tuske S, Birktoft JJ, Ilankumaran P, Ramesha AR, Sayer JM, Jerina DM, Boyer PL, Hughes SH, Arnold E.
Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA.
EMBO J. 21: 6614-24, 2002.
117)  Boyer PL, Sarafianos SG, Arnold E, Hughes SH.
The M184V mutation reduces the selective excision of zidovudine 5'-monophosphate (AZTMP) by the reverse transcriptase of human immunodeficiency virus type 1.
J Virol. 76: 3248-56, 2002.
118)  Barsov EV, Payne WS, Hughes SH.
Adaptation of chimeric retroviruses in vitro and in vivo: isolation of avian retroviral vectors with extended host range.
J Virol. 75: 4973-83, 2001.
119)  Peletskaya EN, Boyer PL, Kogon AA, Clark P, Kroth H, Sayer JM, Jerina DM, Hughes SH.
Cross-linking of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase to template-primer.
J Virol. 75: 9435-45, 2001.
120)  Sarafianos SG, Das K, Tantillo C, Clark AD, Ding J, Whitcomb JM, Boyer PL, Hughes SH, Arnold E.
Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA.
EMBO J. 20: 1449-61, 2001.
121)  Driscoll MD, Golinelli MP, Hughes SH.
In vitro analysis of human immunodeficiency virus type 1 minus-strand strong-stop DNA synthesis and genomic RNA processing.
J Virol. 75: 672-86, 2001.
122)  Hughes SH.
Molecular matchmaking: NNRTIs can enhance the dimerization of HIV type 1 reverse transcriptase.
Proc Natl Acad Sci U S A. 98: 6991-2, 2001.
123)  Julias JG, Ferris AL, Boyer PL, Hughes SH.
Replication of phenotypically mixed human immunodeficiency virus type 1 virions containing catalytically active and catalytically inactive reverse transcriptase.
J Virol. 75: 6537-46, 2001.
124)  Gao HQ, Sarafianos SG, Arnold E, Hughes SH.
RNase H cleavage of the 5' end of the human immunodeficiency virus type 1 genome.
J Virol. 75: 11874-80, 2001.
125)  Boyer PL, Sarafianos SG, Arnold E, Hughes SH.
Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase.
J Virol. 75: 4832-42, 2001.
126)  Golinelli MP, Hughes SH.
Self-priming of retroviral minus-strand strong-stop DNAs.
Virology. 285: 278-90, 2001.
127)  Boyer PL, Gao HQ, Frank P, Clark PK, Hughes SH.
The basic loop of the RNase H domain of MLV RT is important both for RNase H and for polymerase activity.
Virology. 282: 206-13, 2001.
128)  Hsiou Y, Ding J, Das K, Clark AD, Boyer PL, Lewi P, Janssen PA, Kleim JP, Rösner M, Hughes SH, Arnold E.
The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.
J Mol Biol. 309: 437-45, 2001.
129)  Sevilya Z, Loya S, Hughes SH, Hizi A.
The ribonuclease H activity of the reverse transcriptases of human immunodeficiency viruses type 1 and type 2 is affected by the thumb subdomain of the small protein subunits.
J Mol Biol. 311: 957-71, 2001.
130)  Boyer PL, Gao HQ, Clark PK, Sarafianos SG, Arnold E, Hughes SH.
YADD mutants of human immunodeficiency virus type 1 and Moloney murine leukemia virus reverse transcriptase are resistant to lamivudine triphosphate (3TCTP) in vitro.
J Virol. 75: 6321-8, 2001.
131)  Boyer PL, Sarafianos SG, Arnold E, Hughes SH.
Analysis of mutations at positions 115 and 116 in the dNTP binding site of HIV-1 reverse transcriptase.
Proc Natl Acad Sci U S A. 97: 3056-61, 2000.
132)  Boyer PL, Hughes SH.
Effects of amino acid substitutions at position 115 on the fidelity of human immunodeficiency virus type 1 reverse transcriptase.
J Virol. 74: 6494-500, 2000.
133)  Driscoll MD, Hughes SH.
Human immunodeficiency virus type 1 nucleocapsid protein can prevent self-priming of minus-strand strong stop DNA by promoting the annealing of short oligonucleotides to hairpin sequences.
J Virol. 74: 8785-92, 2000.
134)  Pinto VB, Prasad S, Yewdell J, Bennink J, Hughes SH.
Restricting expression prolongs expression of foreign genes introduced into animals by retroviruses.
J Virol. 74: 10202-6, 2000.
135)  Sutrave P, Leferovich JM, Kelly AM, Hughes SH.
The induction of skeletal muscle hypertrophy by a ski transgene is promoter-dependent.
Gene. 241: 107-16, 2000.
136)  Gao HQ, Boyer PL, Sarafianos SG, Arnold E, Hughes SH.
The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase.
J Mol Biol. 300: 403-18, 2000.
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