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Our Science – Hughes Website

Stephen H. Hughes, Ph.D.

Selected Publications
1)  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: 251-9, 2008. [Journal]
2)  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. [Journal]
3)  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. [Journal]
4)  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. [Journal]
5)  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. [Journal]
6)  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: 10943-8, 2008. [Journal]
7)  Oh J, Chang KW, Hughes SH.
Integration of rous sarcoma virus DNA: a CA dinucleotide is not required for integration of the U3 end of viral DNA.
J. Virol. 82: 11480-3, 2008. [Journal]
8)  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. [Journal]
9)  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. [Journal]
10)  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. [Journal]
11)  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. 2008. [Journal]
12)  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. [Journal]
13)  Sarafianos SG, Marchand B, Das K, Himmel D, Parniak MA, Hughes SH, Arnold E.
Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition.
J. Mol. Biol. 2008. [Journal]
14)  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. [Journal]
15)  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. 2008. [Journal]
16)  Hughes S, Crise B.
Using viral vectors in animal research. In: Anthology of Biosafety: X, Animal Biosafety (J.Y. Richmond, ed.). Volume .
.: American Biological Safety Association; 2007. p. 145-166 [Book Chapter]
17)  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. [Journal]
18)  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. [Journal]
19)  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. [Journal]
20)  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. [Journal]
21)  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. [Journal]
22)  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: 4003-15, 2007. [Journal]
23)  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. [Journal]
24)  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. [Journal]
25)  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. [Journal]
26)  Oh J, Chang KW, Alvord WG, Hughes SH.
Alternate polypurine tracts affect rous sarcoma virus integration in vivo.
J. Virol. 80: 10281-4, 2006. [Journal]
27)  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. [Journal]
28)  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. [Journal]
29)  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. [Journal]
30)  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. [Journal]
31)  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. [Journal]
32)  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. [Journal]
33)  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. [Journal]
34)  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. [Journal]
35)  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: 7582-91, 2005. [Journal]
36)  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. [Journal]
37)  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. [Journal]
38)  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. [Journal]
39)  Chang KW, Barsov EV, Ferris AL, Hughes SH.
Mutations of a residue within the polyproline-rich region of Env alter the replication rate and level of cytopathic effects in chimeric avian retroviral vectors.
J. Virol. 79: 10258-67, 2005. [Journal]
40)  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. [Journal]
41)  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: 6112-21, 2004. [Journal]
42)  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. [Journal]
43)  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. [Journal]
44)  Boyer PL, Imamichi T, Sarafianos SG, Arnold E, Hughes SH.
Effects of the Delta67 complex of mutations in human immunodeficiency virus type 1 reverse transcriptase on nucleoside analog excision.
J. Virol. 78: 9987-97, 2004. [Journal]
45)  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. [Journal]
46)  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. [Journal]
47)  Julias JG, Boyer PL, McWilliams MJ, Alvord WG, Hughes SH.
Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis.
Virology. 322: 13-21, 2004. [Journal]
48)  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: 3387-97, 2004. [Journal]
49)  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. [Journal]
50)  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. [Journal]
51)  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 the anti-AIDS drug tenofovir.
Nat. Struct. Mol. Biol. 11: 469-74, 2004. [Journal]
52)  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. [Journal]
53)  Hughes SH.
The RCAS vector system.
Folia Biol. (Praha). 50: 107-19, 2004. [Journal]
54)  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 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 design and discovery. 18: 151-63, 2003. [Journal]
55)  Michejda C, Szekely Z, Hariprakasha H, Hughes S, inventor.
Benzindole Derivatives and Method for Treating HIV/AIDS.
Patent Pending, Filed in October 10, 2006. Pending [Patent]
56)  Hughes S, Boyer P, Linial M, Rinke C, Clark P, inventor.
Foamy Virus Mutant Reverse Transcriptase.
Patent Pending, Filed in July 8, 2004. Pending [Patent]
57)  Hughes S, Sutrave P, Pursel V, inventor.
Enhancement of Musculature in Non-Human Mammals Expressing c-ski.
US Patent: 6,218,596. Issued April 17, 2001. [Patent]
58)  Hughes S, Kumar R, Brumbaugh J, inventor.
Method for the Fluorescent Detection of a DNA Sequence in Real Time.
US Patent: 6,197,499. Issued March 6, 2001. [Patent]
59)  Barsov E, Hughes S, inventor.
Retrovirus Vectors Derived From Avian Sarcoma Leukosis Viruses Permitting Transfer of Genes Into Mammalian Cells.
US Patent: 6,096,534. Issued August 1, 2000. [Patent]
60)  Barsov E, Hughes S, inventor.
Retrovirus Vectors Derived from Avian Sarcoma Leukosis Viruses Permitting Transfer of Genes into Mammalian Cells and Therapeutic Uses Thereof.
US Patent: 6,794,188. September 21, 2004. [Patent]
61)  Ferris A, Hughes S, inventor.
Use of Constitutive Transport Elements for Host Range Control.
US Patent: 6,492,166. Issued December 10, 2002. [Patent]
62)  Hughes S, Salter D, Crittenden L, inventor.
Vectors for Gene Insertion Into Avian Germ Line.
US Patent: 4,997,763. Issued March 5, 1992. [Patent]

This page was last updated on 12/1/2008.