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Nucleoside RT Inhibitors: Structural and Molecular Biology

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Human Immunodeficiency Virus Reverse Transcriptase

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Abstract

Nucleoside analogs were the earliest drugs developed to combat HIV-1 infection. These drugs are taken up by cellular transport systems, activated by cellular kinases, and incorporated into DNA by HIV-1 reverse transcriptase (RT) during the initial stages of viral infection, leading to termination of viral DNA synthesis. This class of anti-HIV drugs has now grown to eight FDA- approved compounds with several more potential drugs in development. Biochemical studies of DNA synthesis by HIV-1 RT and determination of three-dimensional structures of nucleoprotein complexes containing HIV-1 RT have shed light on how changes in enzyme structure can lead to drug resistance. A challenge to developing nucleoside RT inhibitors (NRTIs) and nucleotide RT inhibitors (NtRTIs) is the construction of compounds that will enter cells efficiently and be efficiently converted into the active form of the inhibitor. The intracellular concentrations of the activated drug metabolites and the natural dNTPs are important parts of the equation that determines antiviral activity. The intracellular environments where nucleotide incorporation occurs and where repair of damaged or chain-terminated viral DNA occurs are not well defined and represent a remaining frontier in the further development of drugs that target the dNTP binding site of HIV-1 RT.

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References

  • Abbondanzieri EA, Bokinsky G, Rausch JW, Zhang JX, Le Grice SFJ, Zhuang X (2008) Dynamic binding orientations direct activity of HIV reverse transcriptase. Nature 453(7192):184–189. doi:10.1038/nature06941

    Article  PubMed  CAS  Google Scholar 

  • Acosta-Hoyos AJ, Scott WA (2010) The role of nucleotide excision by reverse transcriptase in HIV drug resistance. Viruses 2(2):372–394

    Article  PubMed  CAS  Google Scholar 

  • Acosta-Hoyos AJ, Matsuura SE, Meyer PR, Scott WA (2012) A role of template cleavage in reduced excision of chain-terminating nucleotides by human immunodeficiency virus type 1 reverse transcriptase containing the M184V mutation. J Virol 86(9):5122–5133. doi:10.1128/JVI.05767-11

    Article  PubMed  CAS  Google Scholar 

  • Arhel NJ, Souquere-Besse S, Munier S, Souque P, Guadagnini S, Rutherford S et al (2007) HIV-1 DNA flap formation promotes uncoating of the pre- integration complex at the nuclear pore. EMBO J 26(12):3025–3037. doi:10.1038/sj.emboj.7601740

    Article  PubMed  CAS  Google Scholar 

  • Arion D, Kaushik N, McCormick S, Borkow G, Parniak MA (1998) Phenotypic mechanism of HIV-1 resistance to 3′-azido-3′-deoxythymidine (AZT): increased polymerization processivity and enhanced sensitivity to pyrophosphate of the mutant viral reverse transcriptase. Biochemistry 37(45):15908–15917

    Article  PubMed  CAS  Google Scholar 

  • Bakshi RP, Hamzeh F, Frank I, Eron JJ Jr, Bosch RJ, Rosenkranz SL et al (2007) Effect of hydroxyurea and dideoxyinosine on intracellular 3′- deoxyadenosine-5′-triphosphate concentrations in HIV-infected patients. AIDS Res Hum Retroviruses 23(11):1360–1365. doi:10.1089/aid.2007.0078

    Article  PubMed  CAS  Google Scholar 

  • Balzarini J, Herdewijn P, De Clercq E (1989) Differential patterns of intracellular metabolism of 2′,3′-didehydro-2′3′-dideoxythymidine and 3′-azido-2′,3′-dideoxythymidine, two potent anti-human immunodeficiency virus compounds. J Biol Chem 264(11):6127–6133

    PubMed  CAS  Google Scholar 

  • Borroto-Esoda K, Myrick F, Feng J, Jeffrey J, Furman P (2004) In vitro combination of amdoxovir and the inosine monophosphate dehydrogenase inhibitors mycophenolic acid and ribavirin demonstrates potent activity against wild-type and drug-resistant variants of human immunodeficiency virus type 1. Antimicrob Agents Chemother 48(11):4387–4394. doi:10.1128/AAC.48.11.4387-4394.2004

    Article  PubMed  CAS  Google Scholar 

  • Boucher CAB, Cammack N, Schipper P, Schuurman R, Rouse P, Wainberg MA, Cameron JM (1993) High-level resistance to (-) enantiomeric 2′-deoxy-3′-thiacytidine in vitro is due to one amino acid substitution in the catalytic site of human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother 37(10):2231–2234

    Article  PubMed  CAS  Google Scholar 

  • Boyer PL, Sarafianos SG, Arnold E, Hughes SH (2001) Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase. J Virol 75(10): 4832–4842

    Article  PubMed  CAS  Google Scholar 

  • Boyer PL, Vu BC, Ambrose Z, Julias JG, Warnecke S, Liao C et al (2009) The nucleoside analogue D-carba T blocks HIV-1 reverse transcription. J Med Chem 52(17):5356–5364

    Article  PubMed  CAS  Google Scholar 

  • Brehm JH, Mellors JW, Sluis-Cremer N (2008) Mechanism by which a glutamine to leucine substitution at residue 509 in the ribonuclease H domain of HIV-1 reverse transcriptase confers zidovudine resistance. Biochemistry 47(52):14020–14027

    Article  PubMed  CAS  Google Scholar 

  • Brehm JH, Scott Y, Koontz DL, Perry S, Hammer S, Katzenstein D, AIDS Clinical Trials Group Study 175 Protocol Team et al (2012) Zidovudine (AZT) monotherapy selects for the A360V mutation in the connection domain of HIV-1 reverse transcriptase. PLoS One 7(2):e31558. doi:10.1371/journal.pone.0031558

    Article  PubMed  CAS  Google Scholar 

  • Chamberlain PP, Ren J, Nichols CE, Douglas L, Lennerstrand J, Larder BA et al (2002) Crystal structures of zidovudine- or lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215. J Virol 76(19):10015–10019

    Article  PubMed  CAS  Google Scholar 

  • Chen R, Wang H, Mansky LM (2002) Roles of uracil-DNA glycosylase and dUTPase in virus replication. J Gen Virol 83(10):2339–2345

    PubMed  CAS  Google Scholar 

  • Chen R, Le Rouzic E, Kearney JA, Mansky LM, Benichou S (2004) Vpr-mediated incorporation of UNG2 into HIV-1 particles is required to modulate the virus mutation rate and for replication in macrophages. J Biol Chem 279(27):28419–28425. doi:10.1074/jbc.M403875200

    Article  PubMed  CAS  Google Scholar 

  • Cihlar T, Ray AS (2010) Nucleoside and nucleotide HIV reverse transcriptase inhibitors: 25 years after zidovudine. Antiviral Res 85(1):39–58. doi:10.1016/j.antiviral.2009.09.014

    Article  PubMed  CAS  Google Scholar 

  • Das K, Bandwar RP, White KL, Feng JY, Sarafianos SG, Tuske S et al (2009) Structural basis for the role of the K65R mutation in HIV-1 reverse transcriptase polymerization, excision antagonism, and tenofovir resistance. J Biol Chem 284(50):35092–35100

    Article  PubMed  CAS  Google Scholar 

  • Das K, Martinez SE, Bauman JD, Arnold E (2012) HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Mol Biol 19(2):253–259. doi:10.1038/nsmb.2223

    Article  PubMed  CAS  Google Scholar 

  • De Clercq E (2011) The clinical potential of the acyclic (and cyclic) nucleoside phosphonates. The magic of the phosphonate bond. Biochem Pharmacol 82(2):99–109. doi:10.1016/j.bcp.2011.03.027

    Article  PubMed  CAS  Google Scholar 

  • Delviks-Frankenberry KA, Nikolenko GN, Pathak VK (2010) The “connection” between HIV drug resistance and RNase H. Viruses 2(7):1476–1503. doi:10.3390/v2071476

    Article  PubMed  CAS  Google Scholar 

  • Diamond TL, Roshal M, Jamburuthugoda VK, Reynolds HM, Merriam AR, Lee KY et al (2004) Macrophage tropism of HIV-1 depends on efficient cellular dNTP utilization by reverse transcriptase. J Biol Chem 279(49):51545–51553. doi:10.1074/jbc.M408573200

    Article  PubMed  CAS  Google Scholar 

  • Ding J, Das K, Hsiou Y, Sarafianos SG, Clark AD Jr, Jacobo-Molina A et al (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 Å resolution. J Mol Biol 284(4):1095–1111. doi:10.1006/jmbi.1998.2208

    Article  PubMed  CAS  Google Scholar 

  • Dismuke DJ, Aiken C (2006) Evidence for a functional link between uncoating of the human immunodeficiency virus type 1 core and nuclear import of the viral preintegration complex. J Virol 80(8):3712–3720. doi:10.1128/JVI.80.8.3712-3720.2006

    Article  PubMed  CAS  Google Scholar 

  • Ehteshami M, Götte M (2008) Effects of mutations in the connection and RNase H domains of HIV-1 reverse transcriptase on drug susceptibility. AIDS Rev 10(4):224–235

    PubMed  Google Scholar 

  • Ehteshami M, Beilhartz GL, Scarth BJ, Tchesnokov EP, McCormick S, Wynhoven B et al (2008) Connection domain mutations N348I and A360V in HIV-1 reverse transcriptase enhance resistance to 3′-azido-3′-deoxythymidine through both RNase H- dependent and -independent mechanisms. J Biol Chem 283(32):22222–22232

    Article  PubMed  CAS  Google Scholar 

  • Faletto MB, Miller WH, Garvey EP, St. Clair MH, Daluge SM, Good SS (1997) Unique intracellular activation of the potent anti-human immunodeficiency virus agent 1592U89. Antimicrob Agents Chemother 41(5):1099–1107

    PubMed  CAS  Google Scholar 

  • Frankel FA, Invernizzi CF, Oliveira M, Wainberg MA (2007) Diminished efficiency of HIV-1 reverse transcriptase containing the K65R and M184V drug resistance mutations. AIDS 21(6):665–675. doi:10.1097/QAD.0b013e3280187505

    Article  PubMed  CAS  Google Scholar 

  • Gallant JE, Parish MA, Keruly JC, Moore RD (2005) Changes in renal function associated with tenofovir disoproxil fumarate treatment, compared with nucleoside reverse-transcriptase inhibitor treatment. Clin Infect Dis 40(8):1194–1198. doi:10.1086/428840

    Article  PubMed  CAS  Google Scholar 

  • Gao W-Y, Shirasaka T, Johns DG, Broder S, Mitsuya H (1993) Differential phosphorylation of azidothymidine, dideoxycytidine, and dideoxyinosine in resting and activated peripheral blood mononuclear cells. J Clin Invest 91(5):2326–2333

    Article  PubMed  CAS  Google Scholar 

  • Gao H-Q, Boyer PL, Sarafianos SG, Arnold E, Hughes SH (2000) The role of steric hindrance in 3TC resistance of human immunodeficiency virus type-1 reverse transcriptase. J Mol Biol 300(2):403–418

    Article  PubMed  CAS  Google Scholar 

  • Gao Y, Lobritz MA, Roth J, Abreha M, Nelson KN, Nankya I et al (2008) Targets of small interfering RNA restriction during human immunodeficiency virus type 1 replication. J Virol 82(6):2938–2951. doi:10.1128/JVI.02126-07

    Article  PubMed  CAS  Google Scholar 

  • García-Lerma JG, Aung W, Cong M-e, Zheng Q, Youngpairoj AS, Mitchell J, Heneine W (2011) Natural substrate concentrations can modulate the prophylactic efficacy of nucleotide HIV reverse transcriptase inhibitors. J Virol 85(13):6610–6617. doi:10.1128/JVI.00311-11

    Article  PubMed  CAS  Google Scholar 

  • Goldstone DC, Ennis-Adeniran V, Hedden JJ, Groom HCT, Rice GI, Christodoulou E et al (2011) HIV-1 restriction factor SAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase. Nature 480(7377):379–382. doi:10.1038/nature10623

    Article  PubMed  CAS  Google Scholar 

  • Götte M (2006) Effects of nucleotides and nucleotide analogue inhibitors of HIV-1 reverse transcriptase in a ratchet model of polymerase translocation. Curr Pharm Des 12(15):1867–1877

    Article  PubMed  Google Scholar 

  • Goujon C, Rivière L, Jarrosson-Wuilleme L, Bernaud J, Rigal D, Darlix J-L, Cimarelli A (2007) SIVSM/HIV-2 Vpx proteins promote retroviral escape from a proteasome- dependent restriction pathway present in human dendritic cells. Retrovirology 4:2. doi:10.1186/1742-4690-4-2

    Article  PubMed  CAS  Google Scholar 

  • Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK, Watt IN, Malim MH (2003) DNA deamination mediates innate immunity to retroviral infection. Cell 113(6):803-–809

    Article  PubMed  CAS  Google Scholar 

  • Hostomsky Z, Hostomska Z, Fu T-B, Taylor J (1992) Reverse transcriptase of human immunodeficiency virus type 1: functionality of subunits of the heterodimer in DNA synthesis. J Virol 66(5):3179–3182

    PubMed  CAS  Google Scholar 

  • Hrecka K, Hao C, Gierszewska M, Swanson SK, Kesik-Brodacka M, Srivastava S, Skowronski J (2011) Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein. Nature 474(7353):658–661. doi:10.1038/nature10195

    Article  PubMed  CAS  Google Scholar 

  • 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(5394):1669–1675

    Article  PubMed  CAS  Google Scholar 

  • Hulme AE, Perez O, Hope TJ (2011) Complementary assays reveal a relationship between HIV-1 uncoating and reverse transcription. Proc Natl Acad Sci USA 108(24):9975–9980. doi:10.1073/pnas.1014522108

    Article  PubMed  CAS  Google Scholar 

  • Jacobo-Molina A, Ding J, Nanni RG, Clark AD Jr, Lu X, Tantillo C et al (1993) Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 Å resolution shows bent DNA. Proc Natl Acad Sci USA 90(13):6320–6324

    Article  PubMed  CAS  Google Scholar 

  • Jamburuthugoda VK, Chugh P, Kim B (2006) Modification of human immunodeficiency virus type 1 reverse transcriptase to target cells with elevated cellular dNTP concentrations. J Biol Chem 281(19):13388–13395. doi:10.1074/jbc.M600291200

    Article  PubMed  CAS  Google Scholar 

  • Jamburuthugoda VK, Santos-Velazquez JM, Skasko M, Operario DJ, Purohit V, Chugh P et al (2008) Reduced dNTP binding affinity of 3TC-resistant M184I HIV-1 reverse transcriptase variants responsible for viral infection failure in macrophage. J Biol Chem 283(14):9206–9216. doi:10.1074/jbc.M710149200

    Article  PubMed  CAS  Google Scholar 

  • Johnson MA, Fridland A (1989) Phosphorylation of 2′,3′-dideoxyinosine by cytosolic 5′- nucleotidase of human lymphoid cells. Mol Pharmacol 36(2):291–295

    PubMed  CAS  Google Scholar 

  • Kaiser SM, Emerman M (2006) Uracil DNA glycosylase is dispensable for human immunodeficiency virus type 1 replication and does not contribute to the antiviral effects of the cytidine deaminase Apobec3G. J Virol 80(2):875–882. doi:10.1128/JVI.80.2.875-882.2006

    Article  PubMed  CAS  Google Scholar 

  • Kati WM, Johnson KA, Jerva LF, Anderson KS (1992) Mechanism and fidelity of HIV reverse transcriptase. J Biol Chem 267(36):25988–25997

    PubMed  CAS  Google Scholar 

  • Kaushik R, Zhu X, Stranska R, Wu Y, Stevenson M (2009) A cellular restriction dictates the permissivity of nondividing monocytes/macrophages to lentivirus and gammaretrovirus infection. Cell Host Microbe 6(1):68–80. doi:10.1016/j.chom.2009.05.022

    Article  PubMed  CAS  Google Scholar 

  • Kellinger MW, Johnson KA (2010) Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptase. Proc Natl Acad Sci USA 107(17):7734–7739. doi:10.1073/pnas.0913946107

    Article  PubMed  CAS  Google Scholar 

  • Kellinger MW, Johnson KA (2011) Role of induced fit in limiting discrimination against AZT by HIV reverse transcriptase. Biochemistry 50(22):5008–5015. doi:10.1021/bi200204m

    Article  PubMed  CAS  Google Scholar 

  • Kennedy EM, Gavegnano C, Nguyen L, Slater R, Lucas A, Fromentin E et al (2010) Ribonucleoside triphosphates as substrate of human immunodeficiency virus type 1 reverse transcriptase in human macrophages. J Biol Chem 285(50):39380–39391. doi:10.1074/jbc.M110.178582

    Article  PubMed  CAS  Google Scholar 

  • Kennedy EM, Daddacha W, Slater R, Gavegnano C, Fromentin E, Schinazi RF, Kim B (2011) Abundant non-canonical dUTP found in primary human macrophages drives its frequent incorporation by HIV-1 reverse transcriptase. J Biol Chem 286(28):25047–25055. doi:10.1074/jbc.M111.234047

    Article  PubMed  CAS  Google Scholar 

  • Kennedy EM, Amie SM, Bambara RA, Kim B (2012) Frequent incorporation of ribonucleotides during HIV-1 reverse transcription and their attenuated repair in macrophages. J Biol Chem 287(17):14280–14288. doi:10.1074/jbc.M112.348482

    Article  PubMed  CAS  Google Scholar 

  • Klarmann GJ, Chen X, North TW, Preston BD (2003) Incorporation of uracil into minus strand DNA affects the specificity of plus strand synthesis initiation during lentiviral reverse transcription. J Biol Chem 278(10):7902–7909. doi:10.1074/jbc.M207223200

    Article  PubMed  CAS  Google Scholar 

  • Kohlstaedt LA, Wang J, Friedman JM, Rice PA, Steitz TA (1992) Crystal structure at 3.5 Å resolution of HIV-1 reverse transcriptase complexed with an inhibitor. Science 256(5065):1783–1790

    Article  PubMed  CAS  Google Scholar 

  • Krokan HE, Drabløs F, Slupphaug G (2002) Uracil in DNA–occurrence, consequences and repair. Oncogene 21(58):8935–8948. doi:10.1038/sj.onc.1205996

    Article  PubMed  CAS  Google Scholar 

  • Laguette N, Sobhian B, Casartelli N, Ringeard M, Chable-Bessia C, Ségéral E et al (2011) SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx. Nature 474(7353):654–657. doi:10.1038/nature10117

    Article  PubMed  CAS  Google Scholar 

  • Lahouassa H, Daddacha W, Hofmann H, Ayinde D, Logue EC, Dragin L et al (2012) SAMHD1 restricts the replication of human immunodeficiency virus type 1 by depleting the intracellular pool of deoxynucleoside triphosphates. Nature Immunol 13(3):223–228. doi:10.1038/ni.2236

    Article  CAS  Google Scholar 

  • Lanier ER, Ptak RG, Lampert BM, Keilholz L, Hartman T, Buckheit RW Jr et al (2010) Development of hexadecyloxypropyl tenofovir (CMX157) for treatment of infection caused by wild-type and nucleoside/nucleotide-resistant HIV. Antimicrob Agents Chemother 54(7):2901–2909

    Article  PubMed  CAS  Google Scholar 

  • Lansdon EB, Samuel D, Lagpacan L, Brendza KM, White KL, Hung M et al (2010) Visualizing the molecular interactions of a nucleotide analog, GS-9148, with HIV-1 reverse transcriptase-DNA complex. J Mol Biol 397(4):967–978. doi:10.1016/j.jmb.2010.02.019

    Article  PubMed  CAS  Google Scholar 

  • Larder BA, Kemp SD, Harrigan PR (1995) Potential mechanism for sustained antiretroviral efficacy of AZT-3TC combination therapy. Science 269(5224):696–699

    Article  PubMed  CAS  Google Scholar 

  • Le Grice SFJ (1993) Human immunodeficiency virus reverse transcriptase. In: Skalka AM, Goff SP (eds) Reverse Transcriptase. Ch. 9. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 163-–191

    Google Scholar 

  • Le Grice SFJ, Naas T, Wohlgensinger B, Schatz O (1991) Subunit-selective mutagenesis indicates minimal polymerase activity in heterodimer-associated p51 HIV-1 reverse transcriptase. EMBO J 10(12):3905–3911

    PubMed  Google Scholar 

  • Lee WA, He G-X, Eisenberg E, Cihlar T, Swaminathan S, Mulato A, Cundy KC (2005) Selective intracellular activation of a novel prodrug of the human immunodeficiency virus reverse transcriptase inhibitor tenofovir leads to preferential distribution and accumulation in lymphatic tissue. Antimicrob Agents Chemother 49(5):1898–1906. doi:10.1128/AAC.49.5.1898-1906.2005

    Article  PubMed  CAS  Google Scholar 

  • Lisziewicz J, Foli A, Wainberg M, Lori F (2003) Hydroxyurea in the treatment of HIV infection: clinical efficacy and safety concerns. Drug Saf 26(9):605–624

    Article  PubMed  CAS  Google Scholar 

  • Maga G, Radi M, Gerard M-A, Botta M, Ennifar E (2010) HIV-1 RT inhibitors with a novel mechanism of action: NNRTIs that compete with the nucleotide substrate. Viruses 2(4):880–899

    Article  PubMed  CAS  Google Scholar 

  • Malim MH (2009) APOBEC proteins and intrinsic resistance to HIV-1 infection. Philos Trans R Soc Lond B Biol Sci 364(1517):675–687. doi:10.1098/rstb.2008.0185

    Article  PubMed  CAS  Google Scholar 

  • Mansky LM, Preveral S, Selig L, Benarous R, Benichou S (2000) The interaction of vpr with uracil DNA glycosylase modulates the human immunodeficiency virus type 1 In vivo mutation rate. J Virol 74(15):7039–7047

    Article  PubMed  CAS  Google Scholar 

  • Marchand B, Götte M (2003) Site-specific footprinting reveals differences in the translocation status of HIV-1 reverse transcriptase. Implications for polymerase translocation and drug resistance. J Biol Chem 278(37):35362–35372

    Article  PubMed  CAS  Google Scholar 

  • Margolis DM, Kewn S, Coull JJ, Ylisastigui L, Turner D, Wise H et al (2002) The addition of mycophenolate mofetil to antiretroviral therapy including abacavir is associated with depletion of intracellular deoxyguanosine triphosphate and a decrease in plasma HIV-1 RNA. J Acquir Immune Defic Syndr 31(1):45–49

    Article  PubMed  CAS  Google Scholar 

  • Markowitz M, Zolopa A, Ruane P, Squires K, Zhong L, Kearney B, Lee W (2011) GS-7340 demonstrates greater declines in HIV-1 RNA than TDF during 14 days of monotherapy in HIV-1-infected subjects. Paper presented at the 18th conference on retroviruses and opportunistic infections. Abstract retrieved from http://www.retroconference.org/2011/Abstracts/42549.htm

  • Menéndez-Arias L (2008) Mechanisms of resistance to nucleoside analogue inhibitors of HIV-1 reverse transcriptase. Virus Res 134(1–2):124–146

    Article  PubMed  CAS  Google Scholar 

  • Meyer PR, Matsuura SE, So AG, Scott WA (1998) Unblocking of chain-terminated primer by HIV-1 reverse transcriptase through a nucleotide-dependent mechanism. Proc Natl Acad Sci USA 95(23):13471–13476

    Article  PubMed  CAS  Google Scholar 

  • Meyer PR, Matsuura SE, Mian AM, So AG, Scott WA (1999) A mechanism of AZT resistance: an increase in nucleotide-dependent primer unblocking by mutant HIV-1 reverse transcriptase. Mol Cell 4(1):35–43

    Article  PubMed  CAS  Google Scholar 

  • Meyer PR, Matsuura SE, Schinazi RF, So AG, Scott WA (2000) Differential removal of thymidine nucleotide analogues from blocked DNA chains by human immunodeficiency virus reverse transcriptase in the presence of physiological concentrations of 2′-deoxynucleoside triphosphates. Antimicrob Agents Chemother 44(12):3465–3472

    Article  PubMed  CAS  Google Scholar 

  • Meyer PR, Rutvisuttinunt W, Matsuura SE, So AG, Scott WA (2007) Stable complexes formed by HIV-1 reverse transcriptase at distinct positions on the primer- template controlled by binding deoxynucleoside triphosphates or foscarnet. J Mol Biol 369(1):41–54

    Article  PubMed  CAS  Google Scholar 

  • Müller B, Restle T, Reinstein J, Goody RS (1991) Interaction of fluorescently labeled dideoxynucleotides with HIV-1 reverse transcriptase. Biochemistry 30(15):3709–3715

    Article  PubMed  Google Scholar 

  • Naesens L, Bischofberger N, Augustijns P, Annaert P, Van den Mooter G, Arimilli MN et al (1998) Antiretroviral efficacy and pharmacokinetics of oral bis(isopropyloxycarbonyloxymethyl)-9-(2-phosphonylmethoxypropyl)adenine in mice. Antimicrob Agents Chemother 42(7):1568–1573

    PubMed  CAS  Google Scholar 

  • Navarro F, Landau NR (2004) Recent insights into HIV-1 Vif. Curr Opin Immunol 16(4):477–482. doi:10.1016/j.coi.2004.05.006

    Article  PubMed  CAS  Google Scholar 

  • Nikolenko GN, Palmer S, Maldarelli F, Mellors JW, Coffin JM, Pathak VK (2005) Mechanism for nucleoside analog-mediated abrogation of HIV-1 replication: balance between RNase H activity and nucleotide excision. Proc Natl Acad Sci USA 102(6):2093–2098

    Article  PubMed  CAS  Google Scholar 

  • Nikolenko GN, Delviks-Frankenberry KA, Palmer S, Maldarelli F, Fivash MJ Jr, Coffin JM, Pathak VK (2007) Mutations in the connection domain of HIV-1 reverse transcriptase increase 3′-azido-3′-deoxythymidine resistance. Proc Natl Acad Sci USA 104(1):317–322. doi:10.1073/pnas.0609642104

    Article  PubMed  CAS  Google Scholar 

  • Painter GR, Almond MR, Trost LC, Lampert BM, Neyts J, De Clercq E et al (2007) Evaluation of hexadecyloxypropyl-9-R-[2- (Phosphonomethoxy)propyl]-adenine, CMX157, as a potential treatment for human immunodeficiency virus type 1 and hepatitis B virus infections. Antimicrob Agents Chemother 51(10):3505–3509

    Article  PubMed  CAS  Google Scholar 

  • Parikh UM, Barnas DC, Faruki H, Mellors JW (2006) Antagonism between the HIV-1 reverse-transcriptase mutation K65R and thymidine-analogue mutations at the genomic level. J Infect Dis 194(5):651–660

    Article  PubMed  CAS  Google Scholar 

  • Parkin NT, Hellmann NS, Whitcomb JM, Kiss L, Chappey C, Petropoulos CJ (2004) Natural variation of drug susceptibility in wild-type human immunodeficiency virus type 1. Antimicrob Agents Chemother 48(2):437–443

    Article  PubMed  CAS  Google Scholar 

  • Pastor-Anglada M, Cano-Soldado P, Molina-Arcas M, Lostao MP, Larráyoz I, Martínez- Picado J, Casado FJ (2005) Cell entry and export of nucleoside analogues. Virus Res 107(2):151–164

    Article  PubMed  CAS  Google Scholar 

  • Perez-Bercoff D, Wurtzer S, Compain S, Benech H, Clavel F (2007) Human immunodeficiency virus type 1: resistance to nucleoside analogues and replicative capacity in primary human macrophages. J Virol 81(9):4540–4550

    Article  PubMed  CAS  Google Scholar 

  • Petrella M, Wainberg MA (2002) Might the M184V substitution in HIV-1 RT confer clinical benefit? AIDS Rev 4(4):224–232

    PubMed  Google Scholar 

  • Petropoulos CJ, Parkin NT, Limoli KL, Lie YS, Wrin T, Huang W et al (2000) A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother 44(4):920–928

    Article  PubMed  CAS  Google Scholar 

  • Powell RD, Holland PJ, Hollis T, Perrino FW (2011) Aicardi-Goutières syndrome gene and HIV-1 restriction factor SAMHD1 is a dGTP-regulated deoxynucleotide triphosphohydrolase. J Biol Chem 286(51):43596–43600. doi:10.1074/jbc.C111.317628

    Article  PubMed  CAS  Google Scholar 

  • Priet S, Gros N, Navarro J-M, Boretto J, Canard B, Quérat G, Sire J (2005) HIV-1- associated uracil DNA glycosylase activity controls dUTP misincorporation in viral DNA and is essential to the HIV-1 life cycle. Mol Cell 17(4):479–490. doi:10.1016/j.molcel.2005.01.016

    Article  PubMed  CAS  Google Scholar 

  • Radzio J, Sluis-Cremer N (2008) Efavirenz accelerates HIV-1 reverse transcriptase ribonuclease H cleavage, leading to diminished zidovudine excision. Mol Pharmacol 73(2):601–606

    Article  PubMed  CAS  Google Scholar 

  • Ray AS, Hostetler KY (2011) Application of kinase bypass strategies to nucleoside antivirals. Antiviral Res 92(2):277–291. doi:10.1016/j.antiviral.2011.08.015

    Article  PubMed  CAS  Google Scholar 

  • Robbins BL, Srinivas RV, Kim C, Bischofberger N, Fridland A (1998) Anti-human immunodeficiency virus activity and cellular metabolism of a potential prodrug of the acyclic nucleoside phosphonate 9-R-(2-phosphonomethoxypropyl)adenine (PMPA), Bis(isopropyloxymethylcarbonyl)PMPA. Antimicrob Agents Chemother 42(3):612–617

    PubMed  CAS  Google Scholar 

  • Rodgers DW, Gamblin SJ, Harris BA, Ray S, Culp JS, Hellmig B et al (1995) The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1. Proc Natl Acad Sci USA 92(4):1222–1226

    Article  PubMed  CAS  Google Scholar 

  • Roy B, Beuneu C, Roux P, Buc H, Lemaire G, Lepoivre M (1999) Simultaneous determination of pyrimidine or purine deoxyribonucleoside triphosphates using a polymerase assay. Anal Biochem 269(2):403–409. doi:10.1006/abio.1999.4051

    Article  PubMed  CAS  Google Scholar 

  • Rutvisuttinunt W, Meyer PR, Scott WA (2008) Interactions between HIV-1 reverse transcriptase and the downstream template strand in stable complexes with primer- template. PLoS One 3(10):e3561

    Article  PubMed  CAS  Google Scholar 

  • Sarafianos SG, Das K, Clark AD Jr, Ding J, Boyer PL, Hughes SH, Arnold E (1999) Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with β-branched amino acids. Proc Natl Acad Sci USA 96(18):10027–10032

    Article  PubMed  CAS  Google Scholar 

  • Sarafianos SG, Clark AD Jr, Das K, Tuske S, Birktoft JJ, Ilankumaran P et al (2002) Structures of HIV-1 reverse transcriptase with pre- and post- translocation AZTMP-terminated DNA. EMBO J 21(23):6614–6624

    Article  PubMed  CAS  Google Scholar 

  • Sarafianos SG, Clark AD Jr, Tuske S, Squire CJ, Das K, Sheng D et al (2003) Trapping HIV-1 reverse transcriptase before and after translocation on DNA. J Biol Chem 278(18): 16280–16288

    Article  PubMed  CAS  Google Scholar 

  • Sarafianos SG, Marchand B, Das K, Himmel DM, Parniak MA, Hughes SH, Arnold E (2009) Structure and function of HIV-1 reverse transcriptase: molecular mechanisms of polymerization and inhibition. J Mol Biol 385(3):693–713

    Article  PubMed  CAS  Google Scholar 

  • Schaller T, Ocwieja KE, Rasaiyaah J, Price AJ, Brady TJ, Roth SL et al (2011) HIV-1 capsid-cyclophilin interactions determining nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog 7(12):e1002439. doi:10.1371/journal.ppat.1002439

    Article  PubMed  CAS  Google Scholar 

  • Schinazi RF, Lloyd RM Jr, Nguyen M-H, Cannon DL, McMillan A, Ilksoy N et al (1993) Characterization of human immunodeficiency viruses resistant to oxathiolane-cytosine nucleosides. Antimicrob Agents Chemother 37(4):875–881

    Article  PubMed  CAS  Google Scholar 

  • Schuurman R, Nijhuis M, van Leeuwen R, Schipper P, de Jong D, Collis P et al (1995) Rapid changes in human immunodeficiency virus type 1 RNA load and appearance of drug-resistant virus populations in persons treated with lamivudine (3TC). J Infect Dis 171(6):1411–1419

    Article  PubMed  CAS  Google Scholar 

  • Sharma B, Kaushik N, Singh K, Kumar S, Pandey VN (2002) Substitution of conserved hydrophobic residues in motifs B and C of HIV-1 RT alters the geometry of its catalytic pocket. Biochemistry 41(52):15685–15697

    Article  PubMed  CAS  Google Scholar 

  • Sheehy AM, Gaddis NC, Choi JD, Malim MH (2002) Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein. Nature 418(6898):646–650. doi:10.1038/nature00939

    Article  PubMed  CAS  Google Scholar 

  • Shirasaka T, Kavlick MF, Ueno T, Gao W-Y, Kojima E, Alcaide ML et al (1995) Emergence of human immunodeficiency virus type 1 variants with resistance to multiple dideoxynucleosides in patients receiving therapy with dideoxynucleosides. Proc Natl Acad Sci USA 92(6): 2398–2402

    Article  PubMed  CAS  Google Scholar 

  • Singh K, Marchand B, Kirby KA, Michailidis E, Sarafianos SG (2010) Structural aspects of drug resistance and Inhibition of HIV-1 reverse transcriptase. Viruses 2(2):606–638

    Article  PubMed  CAS  Google Scholar 

  • Sire J, Quérat G, Esnault C, Priet S (2008) Uracil within DNA: an actor of antiviral immunity. Retrovirology 5:45. doi:10.1186/1742-4690-5-45

    Article  PubMed  CAS  Google Scholar 

  • Sluis-Cremer N, Koontz D, Bassit L, Hernandez-Santiago BI, Detorio M, Rapp KL et al (2009) Anti-human immunodeficiency virus activity, cross-resistance, cytotoxicity, and intracellular pharmacology of the 3′-azido-2′,3′-dideoxypurine nucleosides. Antimicrob Agents Chemother 53(9):3715–3719

    Article  PubMed  CAS  Google Scholar 

  • Smith AJ, Scott WA (2006) The influence of natural substrates and inhibitors on the nucleotide-dependent excision activity of HIV-1 reverse transcriptase in the infected cell. Curr Pharm Des 12(15):1827–1841

    Article  PubMed  CAS  Google Scholar 

  • Smith AJ, Meyer PR, Asthana D, Ashman MR, Scott WA (2005) Intracellular substrates for the primer-unblocking reaction by human immunodeficiency virus type 1 reverse transcriptase: detection and quantitation in extracts from quiescent- and activated-lymphocyte subpopulations. Antimicrob Agents Chemother 49(5):1761–1769

    Article  PubMed  CAS  Google Scholar 

  • Tisdale M, Kemp SD, Parry NR, Larder BA (1993) Rapid in vitro selection of human immunodeficiency virus type 1 resistant to 3′-thiacytidine inhibitors due to a mutation in the YMDD region of reverse transcriptase. Proc Natl Acad Sci USA 90(12):5653–5656

    Article  PubMed  CAS  Google Scholar 

  • Tong W, Lu C-D, Sharma SK, Matsuura S, So AG, Scott WA (1997) Nucleotide- induced stable complex formation by HIV-1 reverse transcriptase. Biochemistry 36(19):5749–5757

    Article  PubMed  CAS  Google Scholar 

  • Tu X, Das K, Han Q, Bauman JD, Clark AD Jr, Hou X et al (2010) Structural basis of HIV-1 resistance to AZT by excision. Nat Struct Mol Biol 17(10):1202–1209

    Article  PubMed  CAS  Google Scholar 

  • Tuske S, Sarafianos SG, Clark AD Jr, Ding J, Naeger LK, White KL et al (2004) Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol 11(5):469–474

    Article  PubMed  CAS  Google Scholar 

  • Van Cor-Hosmer SK, Daddacha W, Kim B (2010) Mechanistic interplay among the M184I HIV-1 reverse transcriptase mutant, the central polypurine tract, cellular dNTP concentrations and drug sensitivity. Virology 406(2):253–260. doi:10.1016/j.virol.2010.07.028

    Article  PubMed  CAS  Google Scholar 

  • Van Cor-Hosmer SK, Daddacha W, Kelly Z, Tsurumi A, Kennedy EM, Kim B (2012) The impact of molecular manipulation in residue 114 of human immunodeficiency virus type-1 reverse transcriptase on dNTP substrate binding and viral replication. Virology 422(2):393–401. doi:10.1016/j.virol.2011.11.004

    Article  PubMed  CAS  Google Scholar 

  • Van Rompay AR, Johansson M, Karlsson A (2000) Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases. Pharmacol Ther 87(2–3):189–198

    Article  PubMed  Google Scholar 

  • Van Rompay AR, Johansson M, Karlsson A (2003) Substrate specificity and phosphorylation of antiviral and anticancer nucleoside analogues by human deoxyribonucleoside kinases and ribonucleoside kinases. Pharmacol Ther 100(2):119–139

    Article  PubMed  CAS  Google Scholar 

  • Vazquez-Padua MA, Kunugi K, Risueno C, Fischer PH (1989) Modulation of the feedback regulation of thymidine kinase activity by pH in 647 V cells. Cancer Res 49(20):5644–5649

    PubMed  CAS  Google Scholar 

  • Whitcomb JM, Parkin NT, Chappey C, Hellmann NS, Petropoulos CJ (2003) Broad nucleoside reverse-transcriptase inhibitor cross-resistance in human immunodeficiency virus type 1 clinical isolates. J Infect Dis 188(7):992–1000. doi:10.1086/378281

    Article  PubMed  CAS  Google Scholar 

  • White KL, Chen JM, Feng JY, Margot NA, Ly JK, Ray AS et al (2006) The K65R reverse transcriptase mutation in HIV-1 reverses the excision phenotype of zidovudine resistance mutations. Antivir Ther 11(2):155–163

    PubMed  CAS  Google Scholar 

  • Willetts KE, Rey F, Agostini I, Navarro J-M, Baudat Y, Vigne R, Sire J (1999) DNA repair enzyme uracil DNA glycosylase is specifically incorporated into human immunodeficiency virus type 1 viral particles through a Vpr-independent mechanism. J Virol 73(2):1682–1688

    PubMed  CAS  Google Scholar 

  • Wurtzer S, Compain S, Benech H, Hance AJ, Clavel F (2005) Effect of cell cycle arrest on the activity of nucleoside analogues against human immunodeficiency virus type 1. J Virol 79(23):14815–14821. doi:10.1128/JVI.79.23.14815-14821.2005

    Article  PubMed  CAS  Google Scholar 

  • Yan N, O’Day E, Wheeler LA, Engelman A, Lieberman J (2011) HIV DNA is heavily uracilated, which protects it from autointegration. Proc Natl Acad Sci USA 108(22):9244–9249. doi:10.1073/pnas.1102943108

    Article  PubMed  CAS  Google Scholar 

  • Yang B, Chen K, Zhang C, Huang S, Zhang H (2007) Virion-associated uracil DNA glycosylase-2 and apurinic/apyrimidinic endonuclease are involved in the degradation of APOBEC3G-edited nascent HIV-1 DNA. J Biol Chem 282(16):11667–11675. doi:10.1074/jbc.M606864200

    Article  PubMed  CAS  Google Scholar 

  • Yap S-H, Sheen C-W, Fahey J, Zanin M, Tyssen D, Lima VD et al (2007) N348I in the connection domain of HIV-1 reverse transcriptase confers zidovudine and nevirapine resistance. PLoS Med 4(12):e335. doi:10.1371/journal.pmed.0040335

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

G.L. and A. J. A-H were supported by predoctoral fellowships from the American Heart Association (2280106 and 0615079B). This work was supported by the US Public Health Service grant AI-39973 to W.A.S. and the University of Miami Developmental Center for AIDS Research (P30-AI-073961).

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Authors and Affiliations

  1. Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33101, USA

    Gaofei Lu & Walter A. Scott

  2. Medicina, Universidad Simón Bolívar, Barranquilla, Atlantico, Colombia

    Antonio J. Acosta-Hoyos

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  1. Gaofei Lu
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  2. Antonio J. Acosta-Hoyos
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  3. Walter A. Scott
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Correspondence to Gaofei Lu .

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  1. , HIV Drug Resistance Program, National Cancer Institute, Frederick, 21702, Maryland, USA

    Stuart LeGrice

  2. McGill University, 3775 University Street 3755, Montreal, H3T 1E2, Québec, Canada

    Matthias Gotte

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Lu, G., Acosta-Hoyos, A.J., Scott, W.A. (2013). Nucleoside RT Inhibitors: Structural and Molecular Biology. In: LeGrice, S., Gotte, M. (eds) Human Immunodeficiency Virus Reverse Transcriptase. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-7291-9_5

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