Stephen H. Hughes

HIV Drug Resistance Program, National Cancer Institute

Affiliated withNational Cancer Institute

Research Area

Biography

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 15	2014

Other Publications

Article	Year
Construction and characterization of a replication-competent retroviral shuttle vector plasmid. Journal of virology\| PubMed ID: 11799171	2002
The M184V mutation reduces the selective excision of zidovudine 5'-monophosphate (AZTMP) by the reverse transcriptase of human immunodeficiency virus type 1. Journal of virology\| PubMed ID: 11884549	2002
Nontemplated base addition by HIV-1 RT can induce nonspecific strand transfer in vitro. Virology\| PubMed ID: 11886271	2002
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 erythroleukemoge... Journal of virology\| PubMed ID: 11932393	2002
Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry\| PubMed ID: 11939780	2002
Nontemplated nucleotide addition by HIV-1 reverse transcriptase. Biochemistry\| PubMed ID: 11980493	2002
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. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12093908	2002
Mutation of the catalytic domain of the foamy virus reverse transcriptase leads to loss of processivity and infectivity. Journal of virology\| PubMed ID: 12097569	2002
Nucleoside analog resistance caused by insertions in the fingers of human immunodeficiency virus type 1 reverse transcriptase involves ATP-mediated excision. Journal of virology\| PubMed ID: 12186898	2002
Structures of HIV-1 reverse transcriptase with pre- and post-translocation AZTMP-terminated DNA. The EMBO journal\| PubMed ID: 12456667	2002
Trapping HIV-1 reverse transcriptase before and after translocation on DNA. The Journal of biological chemistry\| PubMed ID: 12554739	2003
A novel mechanism for inhibition of HIV-1 reverse transcriptase. Bioorganic chemistry\| PubMed ID: 12642128	2002
Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole ana... Journal of medicinal chemistry\| PubMed ID: 12723956	2003
Secondary structure in the nucleic acid affects the rate of HIV-1 nucleocapsid-mediated strand annealing. Biochemistry\| PubMed ID: 12846564	2003
A conformationally locked analogue of the anti-HIV agent stavudine. An important correlation between pseudorotation and maximum amplitude. Journal of medicinal chemistry\| PubMed ID: 12852759	2003
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. Journal of virology\| PubMed ID: 12857924	2003
On the detection of multiple-binding modes of ligands to proteins, from biological, structural, and modeling data. Journal of computer-aided molecular design\| PubMed ID: 13677481	2003
Mutations in the 5' end of the human immunodeficiency virus type 1 polypurine tract affect RNase H cleavage specificity and virus titer. Journal of virology\| PubMed ID: 14512562	2003
Roles of viral and cellular proteins in the expression of alternatively spliced HTLV-1 pX mRNAs. Virology\| PubMed ID: 14675632	2003
PCR amplification of DNA containing non-standard base pairs by variants of reverse transcriptase from Human Immunodeficiency Virus-1. Nucleic acids research\| PubMed ID: 14757837	2004
Nonnucleoside inhibitor binding affects the interactions of the fingers subdomain of human immunodeficiency virus type 1 reverse transcriptase with DNA. Journal of virology\| PubMed ID: 15016861	2004
Mutations at position 184 of human immunodeficiency virus type-1 reverse transcriptase affect virus titer and viral DNA synthesis. Virology\| PubMed ID: 15063112	2004
Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nature structural & molecular biology\| PubMed ID: 15107837	2004
Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly poten... Journal of medicinal chemistry\| PubMed ID: 15115397	2004
Characterization of the polymerase and RNase H activities of human foamy virus reverse transcriptase. Journal of virology\| PubMed ID: 15163704	2004
Designing anti-AIDS drugs targeting the major mechanism of HIV-1 RT resistance to nucleoside analog drugs. The international journal of biochemistry & cell biology\| PubMed ID: 15183339	2004
Identification of glycosylation sites in the SU component of the Avian Sarcoma/Leukosis virus Envelope Glycoprotein (Subgroup A) by mass spectrometry. Virology\| PubMed ID: 15262505	2004
Effects of the Delta67 complex of mutations in human immunodeficiency virus type 1 reverse transcriptase on nucleoside analog excision. Journal of virology\| PubMed ID: 15331732	2004
The RCAS vector system. Folia biologica\| PubMed ID: 15373344	2004
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. Journal of medicinal chemistry\| PubMed ID: 15456247	2004
Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage. Journal of virology\| PubMed ID: 15542682	2004
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 ... Drug design and discovery\| PubMed ID: 15553926	2003
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 m... Journal of virology\| PubMed ID: 15564466	2004
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... Progress in biophysics and molecular biology\| PubMed ID: 15572156	2005
Fixed conformation nucleoside analogs effectively inhibit excision-proficient HIV-1 reverse transcriptases. Journal of molecular biology\| PubMed ID: 15581889	2005
Taking aim at a moving target: designing drugs to inhibit drug-resistant HIV-1 reverse transcriptases. Current opinion in structural biology\| PubMed ID: 15582396	2004
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, r... Journal of medicinal chemistry\| PubMed ID: 15771434	2005
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. Journal of virology\| PubMed ID: 16051819	2005
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. Journal of virology\| PubMed ID: 16227289	2005
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 ... Journal of medicinal chemistry\| PubMed ID: 16302798	2005
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. Journal of virology\| PubMed ID: 16352569	2006
Combining mutations in HIV-1 reverse transcriptase with mutations in the HIV-1 polypurine tract affects RNase H cleavages involved in PPT utilization. Virology\| PubMed ID: 16473384	2006
The level of reverse transcriptase (RT) in human immunodeficiency virus type 1 particles affects susceptibility to nonnucleoside RT inhibitors but not to lamivudine. Journal of virology\| PubMed ID: 16474164	2006
Why do HIV-1 and HIV-2 use different pathways to develop AZT resistance? PLoS pathogens\| PubMed ID: 16485036	2006
The history of N-methanocarbathymidine: the investigation of a conformational concept leads to the discovery of a potent and selective nucleoside antiviral agent. Antiviral research\| PubMed ID: 16730077	2006
Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap. Journal of virology\| PubMed ID: 17005648	2006
Alternate polypurine tracts affect rous sarcoma virus integration in vivo. Journal of virology\| PubMed ID: 17005708	2006
Crystal structures of clinically relevant Lys103Asn/Tyr181Cys double mutant HIV-1 reverse transcriptase in complexes with ATP and non-nucleoside inhibitor HBY 097. Journal of molecular biology\| PubMed ID: 17056061	2007
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\| PubMed ID: 17123564	2007
Analysis of amino acids in the beta7-beta8 loop of human immunodeficiency virus type 1 reverse transcriptase for their role in virus replication. Journal of molecular biology\| PubMed ID: 17141805	2007
HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site. ACS chemical biology\| PubMed ID: 17184135	2006
Human T-cell leukemia virus type 1 integration target sites in the human genome: comparison with those of other retroviruses. Journal of virology\| PubMed ID: 17409138	2007
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. Journal of molecular biology\| PubMed ID: 17597154	2007
In vitro fidelity of the prototype primate foamy virus (PFV) RT compared to HIV-1 RT. Virology\| PubMed ID: 17631930	2007
Transduction of rhesus macaque hematopoietic stem and progenitor cells with avian sarcoma and leukosis virus vectors. Human gene therapy\| PubMed ID: 17655493	2007
Targeting to the endoplasmic reticulum improves the folding of recombinant human telomerase reverse transcriptase. Protein expression and purification\| PubMed ID: 17658270	2007
Synthesis, biological activity, and crystal structure of potent nonnucleoside inhibitors of HIV-1 reverse transcriptase that retain activity against mutant forms of the enzyme. Journal of medicinal chemistry\| PubMed ID: 17663538	2007
Rous sarcoma virus (RSV) integration in vivo: a CA dinucleotide is not required in U3, and RSV linear DNA does not autointegrate. Journal of virology\| PubMed ID: 17959663	2008
Mutations in the U5 region adjacent to the primer binding site affect tRNA cleavage by human immunodeficiency virus type 1 reverse transcriptase in vivo. Journal of virology\| PubMed ID: 17989171	2008
2,3-dihydro-6,7-dihydroxy-1H-isoindol-1-one-based HIV-1 integrase inhibitors. Journal of medicinal chemistry\| PubMed ID: 18095643	2008
Oncogenicity of DNA in vivo: tumor induction with expression plasmids for activated H-ras and c-myc. Biologicals : journal of the International Association of Biological Standardization\| PubMed ID: 18218323	2008
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. The Journal of biological chemistry\| PubMed ID: 18218634	2008
High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: strategic flexibility explains potency against resistance mutations. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18230722	2008
D-(+)-iso-methanocarbathymidine: a high-affinity substrate for herpes simplex virus 1 thymidine kinase. ChemMedChem\| PubMed ID: 18399509	2008
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... Journal of virology\| PubMed ID: 18562520	2008
Reduced genotoxicity of avian sarcoma leukosis virus vectors in rhesus long-term repopulating cells compared to standard murine retrovirus vectors. Molecular therapy : the journal of the American Society of Gene Therapy\| PubMed ID: 18578011	2008
HIV-1 reverse transcriptase connection subdomain mutations reduce template RNA degradation and enhance AZT excision. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18667707	2008
Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design. Nucleic acids research\| PubMed ID: 18676450	2008
Integration of rous sarcoma virus DNA: a CA dinucleotide is not required for integration of the U3 end of viral DNA. Journal of virology\| PubMed ID: 18768972	2008
Synthesis of conformationally locked carbocyclic nucleoside phosphonates to probe the active site of HIV-1 RT. Nucleic acids symposium series (2004)\| PubMed ID: 18776534	2008
Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. Journal of molecular biology\| PubMed ID: 19022262	2009
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. Bioorganic & medicinal chemistry letters\| PubMed ID: 19364649	2009
North- and south-bicyclo[3.1.0]hexene nucleosides: the effect of ring planarity on anti-HIV activity. ChemMedChem\| PubMed ID: 19533724	2009
The nucleoside analogue D-carba T blocks HIV-1 reverse transcription. Journal of medicinal chemistry\| PubMed ID: 19678643	2009
Mutations in the thumb allow human immunodeficiency virus type 1 reverse transcriptase to be cleaved by protease in virions. Journal of virology\| PubMed ID: 19759158	2009
Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance. The Journal of biological chemistry\| PubMed ID: 19812032	2009
Structure of HIV-1 reverse transcriptase with the inhibitor beta-Thujaplicinol bound at the RNase H active site. Structure (London, England : 1993)\| PubMed ID: 20004166	2009
Lens epithelium-derived growth factor fusion proteins redirect HIV-1 DNA integration. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20133638	2010
Flexible use of nuclear import pathways by HIV-1. Cell host & microbe\| PubMed ID: 20227665	2010
Tumors induced in mice by direct inoculation of plasmid DNA expressing both activated H-ras and c-myc. International journal of biological sciences\| PubMed ID: 20376206	2010
Nature, position, and frequency of mutations made in a single cycle of HIV-1 replication. Journal of virology\| PubMed ID: 20660205	2010
Structural basis of HIV-1 resistance to AZT by excision. Nature structural & molecular biology\| PubMed ID: 20852643	2010
Foamy retrovirus integrase contains a Pol dimerization domain required for protease activation. Journal of virology\| PubMed ID: 21123385	2011
4'-C-methyl-2'-deoxyadenosine and 4'-C-ethyl-2'-deoxyadenosine inhibit HIV-1 replication. Antimicrobial agents and chemotherapy\| PubMed ID: 21343443	2011
Development of tricyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors. Bioorganic & medicinal chemistry letters\| PubMed ID: 21493066	2011
Structural and functional analyses of the second-generation integrase strand transfer inhibitor dolutegravir (S/GSK1349572). Molecular pharmacology\| PubMed ID: 21719464	2011
The effects of RNase H inhibitors and nevirapine on the susceptibility of HIV-1 to AZT and 3TC. Virology\| PubMed ID: 21907380	2011
Protein delivery using engineered virus-like particles. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 21949376	2011
Molecular dynamics approaches estimate the binding energy of HIV-1 integrase inhibitors and correlate with in vitro activity. Antimicrobial agents and chemotherapy\| PubMed ID: 22037850	2012
Mutagenesis of human immunodeficiency virus reverse transcriptase p51 subunit defines residues contributing to vinylogous urea inhibition of ribonuclease H activity. The Journal of biological chemistry\| PubMed ID: 22105069	2012
Bicyclic hydroxy-1H-pyrrolopyridine-trione containing HIV-1 integrase inhibitors. Chemical biology & drug design\| PubMed ID: 22107736	2012
Human immunodeficiency virus type 1 capsid mutation N74D alters cyclophilin A dependence and impairs macrophage infection. Journal of virology\| PubMed ID: 22301145	2012
HIV-1 and HIV-2 reverse transcriptases: different mechanisms of resistance to nucleoside reverse transcriptase inhibitors. Journal of virology\| PubMed ID: 22438533	2012
HIV-1 reverse transcription. Cold Spring Harbor perspectives in medicine\| PubMed ID: 23028129	2012
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... Nucleic acids research\| PubMed ID: 23042676	2012
Activities, crystal structures, and molecular dynamics of dihydro-1H-isoindole derivatives, inhibitors of HIV-1 integrase. ACS chemical biology\| PubMed ID: 23075516	2013
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. Journal of virology\| PubMed ID: 23097450	2013
6,7-Dihydroxy-1-oxoisoindoline-4-sulfonamide-containing HIV-1 integrase inhibitors. Bioorganic & medicinal chemistry letters\| PubMed ID: 23149229	2012
A comparison of the ability of rilpivirine (TMC278) and selected analogues to inhibit clinically relevant HIV-1 reverse transcriptase mutants. Retrovirology\| PubMed ID: 23217210	2012
Identification of a 3-aminoimidazo[1,2-a]pyridine inhibitor of HIV-1 reverse transcriptase. Virology journal\| PubMed ID: 23231773	2012
H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell\| PubMed ID: 23452851	2013
A homology model of HIV-1 integrase and analysis of mutations designed to test the model. Journal of molecular biology\| PubMed ID: 23542006	2013
Mutations in HIV-1 reverse transcriptase cause misfolding and miscleavage by the viral protease. Virology\| PubMed ID: 23850459	2013
Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23959861	2013
Effects of substitutions at the 4' and 2 positions on the bioactivity of 4'-ethynyl-2-fluoro-2'-deoxyadenosine. Antimicrobial agents and chemotherapy\| PubMed ID: 24100493	2013
Discovery of Novel Inhibitors of HIV-1 Reverse Transcriptase Through Virtual Screening of Experimental and Theoretical Ensembles. Chemical biology & drug design\| PubMed ID: 24405985	2014
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... Journal of medicinal chemistry\| PubMed ID: 24471816	2014
False-positive HIV PCR test following ex vivo lentiviral gene transfer treatment of X-linked severe combined immunodeficiency vector. Molecular therapy : the journal of the American Society of Gene Therapy\| PubMed ID: 24487563	2014
Enhancers are major targets for murine leukemia virus vector integration. Journal of virology\| PubMed ID: 24501411	2014