Two DNA polymerases: HIV reverse transcriptase and the Klenow fragment of Escherichia coli DNA polymerase I.
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Amino Acid Sequence↗
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Pharmacodynamic studies (PD) of didanosine (ddI) alone and in combination with azidothymidine (AZT) in human T-cells; a stochastic biochemical approach to antiretroviral nucleoside drug combination in inhibiting HIV-reverse transcriptase (RT).
Didanosine (ddI) is used in the treatment of HIV-1 infection alone and in combination with azidothymidine (AZT). When combined with AZT, patients exhibit improved patterns of surrogate markers after sequential combination regimens of ddI and AZT compared to either drug monotherapy. We have investigated the biochemical mechanism(s) of this synergistic drug combination in human PBMC cells and in human T-cell lines sensitive and resistant to AZT due to lack of thymidine kinase (TK). DdI is preferentially activated to its triphosphate anabolite, ddATP, at 3:1 ratio in human T-lymphocytes compared to monocytes from the same individual. There are no apparent differences in the intracellular concentrations of ddATP in Jurkat/0 and Jurkat/AZT-10, an AZT resistant human T-cell line, when ddI is administered alone or in combination with AZT, hence there appears to be a case of collateral sensitivity. Intracellular increases of AZTTP concentrations in patient's PBMC cells have been determined clinically after AZT alone and in a combination regimen with ddI. A stochastic biochemical model has been developed that estimates the velocity of HIV-RT under uninhibited and inhibited conditions by the active anabolites, AZTTP and ddATP. This model provides a rational explanation for the greater inhibition of HIV-RT in the presence of both inhibitors, AZTTP and ddATP, as compared to the presence of either anabolite triphosphate alone. Expanding this model to describe the inhibition of HIV-RT in the presence of three competitive inhibitors, AZTTP, ddATP and 3TCTP demonstrated that the presence of these HIV-RT inhibitors resulted in an even greater inhibition of this viral enzyme necessary for HIV integration and replication. Hence, a more effective inhibition of HIV-RT enzyme is achieved by the combination of the three drugs, AZT, ddl and 3TC. In an effort to verify this model with experimental data the kinetics of HIV-RT were studied in the absence and after inhibition by AZTTP or ddATP alone, both AZTTP + ddATP or AZTTP + ddATP + 3TCTP. Treatment of HIV-RT with high concentrations of these triphosphate inhibitors, as high as 3Kis, inhibited this enzyme to greater than 90% of untreated control. However, a small percentage of residual HIV-RT, 6%, was uninhibited even after exposure to 3Ki concentrations of each inhibitor. These studies strongly suggested that: 1) AZT plus ddI or AZT plus ddI plus 3TC are synergistic at the active anabolite level against HIV-RT; 2) the combination of the three nucleoside analog drugs (AZT, ddI 3TC) is needed for more effective inhibition of HIV-RT; 3) that the combination of the triphosphates at concentrations much greater than those pharnacologically achieved in T-Cells or PBMC under treatment conditions did not inhibit completely HIV-RT. Hence, the three nucleoside HIV-RT inhibitors must be combined with other classes of antiviral drugs or T-cell specific inhibitor drugs.
Anti-HIV Agents↗
The thumb domain of the P51-subunit is essential for activation of HIV reverse transcriptase.
The biologically relevant and active form of human immunodeficiency virus reverse transcriptase is a heterodimer produced in a two-step dimerization process. Dimerization involves first the rapid association of the two subunits, followed by a slow conformational change yielding a fully active form. In the present study, we demonstrate that the interaction between the thumb domain of p51 and the RNase-H domain of p66 plays a major role in an essential conformational change required for proper folding of the primer/template and the tRNA-binding site, for maturation and for activation of heterodimeric reverse transcriptase. A synthetic peptide derived from the sequence within the thumb domain of p51, which forms the interface with the RNase-H domains of p66, binds heterodimeric reverse transcriptase with an apparent dissociation constant in the nanomolar range and selectively inhibits activation of heterodimeric reverse transcriptase with an inhibition constant of 1.2 microM. A detailed study of the mechanism of inhibition reveals that this peptide does not require dissociation of heterodimeric RT for efficient inhibition and does not affect subunit association, but interferes with the conformational change required for activation of heterodimeric reverse transcriptase, resulting in a decrease in the affinity of reverse transcriptase for the tRNA and an increase in the stability of the primer/template/reverse transcriptase complex. We have previously proposed that the dimeric nature of reverse transcriptase represents an interesting target for the design of antiviral agents. On the basis of this work, we propose that the conformational changes involved in the activation of reverse transcriptase similarly represent an important target for the design of novel antiviral compounds.
Amino Acid Sequence↗
Inhibition of HIV-1 reverse transcriptase and HIV-1 replication by Calophyllum coumarins and xanthones.
As part of our continuing study on the Calophyllum species, a number of coumarins, xanthones and chromene acids from different Calophyllum species of Sri Lanka were tested for inhibitory activity against the HIV-1 and its virally-encoded reverse transcriptase (RT). These compounds were found to be inactive in both the HIV-1 RT and whole virus systems. In contrast, cordatolide A and B demonstrated IC(50) values of 19.3 and 11.7 microM, respectively, against HIV-1 replication in a novel green fluorescent protein (GFP)-based reporter cell assay (HOG.R5).
Anti-HIV Agents↗
Inhibitory effects of Egyptian folk medicines on human immunodeficiency virus (HIV) reverse transcriptase.
Extracts of 41 medicinal plants used in Egyptian folk medicine were screened for their inhibitory effects on human immunodeficiency virus-1 reverse transcriptase. The extracts of fruits of Phyllanthus emblica, Quercus pedunculata, Rumex cyprius, Terminalia bellerica, Terminalia chebula and Terminalia horrida showed significant inhibitory activity with IC50 < or = 50 micrograms/ml. Through a bioassay guided-fractionation of the methanol extract of the fruit of P. emblica, putranjivain A (1) was isolated as a potent inhibitory substance with IC50 = 3.9 microM, together with 1,6-di-O-galloyl-beta-D-glucose (2), 1-O-galloyl-beta-D-glucose (3), kaempferol-3-O-beta-D-glucoside (4), quercetin-3-O-beta-D-glucoside (5) and digallic acid (6). The inhibitory mode of action by 1, 2 and 6 was non-competitive with respect to the substrate but competitive with respect to a template-primer. Furthermore, the stereochemistry of 1 was established in this paper by nuclear magnetic resonance spectroscopy.
Carbohydrate Conformation↗
Mechanism and fidelity of HIV reverse transcriptase.
We have examined the RNA-dependent and DNA-dependent polymerase and ribonuclease H catalytic activities of human immunodeficiency virus reverse transcriptase using rapid transient kinetic methods with defined synthetic 25/45-mer DNA/RNA and DNA/DNA primer/templates. The Kd value for interaction of the enzyme with duplex DNA was 4.7 nM, and the value for RNA/DNA heteroduplex was of similar magnitude. A pre-steady state burst of nucleoside triphosphate incorporation was observed for both DNA and RNA templates. Analysis of the dATP concentration dependence of the burst rate provided Kd values for dATP of 4 and 14 microM and maximum rates of single nucleotide incorporation, kpol, of 33 and 74 s-1, for DNA and RNA templates, respectively. Subsequent turnovers were limited by the rate of dissociation of the primer/template from the enzyme at rates of 0.18 and 0.06 s-1 for duplex DNA and RNA/DNA heteroduplex, respectively. Analysis of rates of DNA polymerization and RNA cleavage using the RNA template revealed that the two activities are independent of one another. The polymerization rate (4-70 s-1) was dependent on dATP concentration, whereas the RNA cleavage occurred at a constant rate of 10 s-1 over the 100-fold dATP concentration range (2-200 microM). Examination of the RNA cleavage products resulting from a single turnover indicates that the polymerase and ribonuclease domains of the enzyme are separated by a distance corresponding to 19 bases of RNA/DNA heteroduplex, consistent with the recently published crystal structure (Kohlstaedt, L. A., Wang, J., Friedman, J., Rice, P. A., and Steitz, T. A. (1992) Science 256, 1783-1790). Analysis of the kinetics of processive synthesis suggested that the initial binding of dNTP leads to a faster rate of dissociation of DNA from the enzyme. Further investigation supported a two-step dNTP binding mechanism with the formation of an initial E.DNA.dNTP complex followed by a more stable E'.DNA.dNTP complex. The Kd values for incorporation of incorrect nucleoside triphosphates opposite a DNA template thymidine were 1010 microM for dGTP, 1240 microM for dCTP, and 840 microM for dTTP. The corresponding maximum kpol rates were 4.8 s-1 for dGTP, 0.52 s-1 for dCTP, and 0.41 s-1 for dTTP. These values provide fidelity estimates of 1740 for discrimination against dGTP, 19,700 for dCTP, and 16,900 for dTTP misincorporations at this site.
Base Sequence↗
Inhibition of HIV reverse transcriptase by 2',3'-dideoxynucleoside triphosphates.
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DNA↗
Identification of key mutations in HIV reverse transcriptase gene can influence the clinical outcome of HAART.
Therapeutic failures due to in vivo loss of drug sensitivity are still a major problem in AIDS care. Currently, the role of and methods for detecting resistant mutant strains in patients before therapeutic choices are still under debate. To investigate the relevance of screening for key mutations alone the commercial INNO-LiPA HIV-1 RT method was applied retrospectively to analyzing several HIV codons correlated with resistance to RTI (reverse-transcriptase inhibitors) in sera from 62 patients before starting HAART protocols, selected on the basis of clinical parameters. INNO-LiPA detected several resistant mutant strains, which were strictly consistent with previous selective pressure in the patients. A significant correlation between genotype pattern and response to HAART was found. The presence of key mutations associated with resistance to one or two RTI included in the protocol correlated with a decrease in treatment benefits, whereas patients with wild-type or non-resistant viral strains exhibited better response to HAART. Even if this information had been available when treatment was started, 45 of the patients would not have received different treatment. When compared with the total number of patients, the subgroup receiving a treatment that was considered retrospectively as consistent with the key mutation pattern exhibited a significantly better outcome. Although the interpretation of resistance-related key mutations needs improvement, this surrogate LiPA method seems to maintain a predictive role in the management of HIV infection, and is less expensive.
Anti-HIV Agents↗
Sequence-specific actinomycin D binding to single-stranded DNA inhibits HIV reverse transcriptase and other polymerases.
Primer extension assays using recombinant templates constructed to contain all 256 possible base quartets in a minimum length sequence were used to examine binding of the anticancer drug actinomycin D to single-stranded DNA. Single-stranded templates were generated by digestion of linearized plasmid with the double-strand-specific T7 gene 6 exonuclease. Actinomycin D formed high-affinity, kinetically stable complexes that paused primer elongation at specific sites by HIV-1 reverse transcriptase, Sequenase (modified T4 DNA polymerase), the Klenow fragment of Escherichia coli DNA polymerase, and Vent (exo-) DNA polymerase. Pauses occurred most commonly near G+C-rich nucleotide clusters, including GpC steps, the preferred sites of double-stranded DNA binding. Complexes were stable for several minutes at temperatures over 50 degrees C as determined by their abilities to pause Vent polymerase at elevated temperatures. Significant variations were noted in pause patterns of different polymerases, demonstrating differential responses of polymerases to a bound actinomycin. Covalent adducts formed on template DNA by a photoaffinity analog of actinomycin D completely stopped primer extension. These results support the possibility that actinomycin D inhibits transcription elongation by complexing single-stranded DNA in the open transcription complex. Single-stranded DNA binding by actinomycin D or analogs may also provide routes for combating HIV or other viruses which replicate through single-stranded intermediates.
Base Composition↗
Targeting HIV reverse transcriptase in novel ways.
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Antiviral Agents↗
RNase H activity of HIV reverse transcriptases is confined exclusively to the dimeric forms.
A method for the rapid preparation of a defined substrate to monitor RNase H activity has been developed. Using this substrate, we have investigated the RNase H activities of the different forms of recombinant HIV-1 and HIV-2 reverse transcriptase (RT) in detail. As we report here, RNase H activity is associated only with the dimeric forms (p51/p66 or p66/p66) of the enzymes.
Amino Acid Sequence↗
HIV-1 reverse transcriptase mutations found in a drug-experienced patient confer reduced susceptibility to multiple nucleoside reverse transcriptase inhibitors.
HIV-1 reverse transcriptase (RT) genotypes were obtained from 13 patients treated with stavudine. No previously-reported mutations indicative of stavudine resistance were found in these patients and no novel mutations occurred in more than two patients. One patient, treated with stavudine for 1 month and treated previously with zidovudine, zalcitabine and lamivudine, carried a mutation at codon 75 of the RT (V75M). A chimeric virus, including the patient's RT sequence from codon 25 to codon 220, which carried the resistance mutations M41 L, D67N, T69D, K70R, L210W and T215Y in addition to V75M, displayed reduced susceptibility to multiple nucleoside RT inhibitors (NRTIs). Removal of V75M from this RT background resulted in a return of susceptibility to didanosine and lamivudine. Our data are in agreement with previous studies demonstrating the rarity of stavudine resistance mutations in stavudine-treated patients. However, we describe a new set of mutations, found in the RT of a heavily-treated patient, that can confer reduced susceptibility to multiple NRTIs. These results underscore the importance of increased vigilance for possible multiple-drug resistance in patients who have been heavily treated with NRTIs.
Acquired Immunodeficiency Syndrome↗
Mammalian tRNA(Lys)3 and pre-tRNA(Lys)3 variants as primers and inhibitors of viral cDNA synthesis by HIV reverse transcriptase in vitro.
We constructed a set of mammalian tRNA(Lys)3-pseudogenes, whose pre-tRNAs are processing-deficient in HeLa extract. The 3'-flanking region was designed partially or completely complementary to the PBS-flanking nucleotides of the U5-region of HIV-1 genomic RNA. We show that only the pre-tRNA with completely hybridized 3'-flanking region is efficiently extended by the HIV-1 reverse transcriptase, whereas the partially complementary pre-tRNA(Lys)3, the 3'-terminal 10 nucleotides of which are not hybridized to the viral template, is unable to prime the cDNA-synthesis.
Animals↗
Characterization and clinical association of antibody inhibitory to HIV reverse transcriptase activity.
Reverse transcriptase activity of the human immunodeficiency virus (HIV) was blocked in vitro by immunoglobulin G (IgG) derived from certain individuals infected with this retrovirus. A heterogeneous immune response for inhibition of enzyme function was noted. Catalytic activity was depressed by 50% or more with the use of 10 micrograms of IgG from 11 of 16 HIV-seropositive asymptomatic carriers, but from 0 of 8 seronegative controls and 2 of 12 patients with acquired immune deficiency syndrome (AIDS) or the AIDS-related complex (ARC). The inhibitor was confined to the F(ab')2 fragment. It was not directed against the poly(rA) X oligo(dT) template, nor against major envelope or structural viral antigens, and did not cross-react with bacterial, avian, or other mammalian DNA polymerases. It did not correlate with recognition of polymerase antigens by radioimmunoprecipitation. Loss of this inhibitor may be associated with development of clinical disease. Ten asymptomatic HIV-seropositive carriers with high titers of IgG antibodies to reverse transcriptase were followed for a mean of 3 years. All of four lost inhibitory capability prior to development of AIDS or ARC, while titers persist in the six who remain clinically healthy.
AIDS-Related Complex↗
Chemical process evolution of efavirenz, a potent non-nucleosidal HIV reverse transcriptase inhibitor.
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Alkynes↗
Pyridazines 82. Synthesis of pyridazino [3,4-b][1,5]benzodiazepin-5-ones and their biological evaluation as non-nucleoside HIV reverse transcriptase inhibitors.
Starting from 3,6-dichloro-N-(2-chloro-5-nitrophenyl)-pyridazine-4-carboxamide (7) a series of 6,11-dialkylated pyridazino- [3,4-b][1,5]benzodiazepin-5-ones with a 3-chloro-8-nitro, 8-amino, 8-acetylamino, or 8-chloro substitution pattern was prepared via N-alkyl-3-alkylamino-6-chloro-N-(2-chloro-5-nitrophenyl) -pyridazine-4-carboxamides. The new compounds were screened as non-nucleoside reverse transcriptase inhibitors. The influence of the substitution pattern in compounds 10-13 on inhibitory potency is discussed.
Anti-HIV Agents↗
Inhibition of HIV-reverse transcriptase activity by asterriquinone and its analogues.
Asterriquinone (ARQ; 2,5-bis-[1'-(1", 1"-dimethyl-2"-propenyl)- indol-3'-yl]-3,6-dihydroxy-1,4-benzoquinone) and its three analogues [i.e., 3,6-dihydroxy-2-[2'-(1", 1"-dimethyl-2"-propenyl)-indol-3'-yl]-5-[1', 7'- (1",1"-dimethylpropano)-indol-3'-yl]-1,4-benzoquinone (B1-4), 3,6-dihydroxy-2-[2'-(1", 1"-dimethyl-2"-propenyl)-indol-3'-yl]-5-indol-3'-yl-1,4-benzoquinone (C1-1) and 3,6-dihydroxy-2,5-diindol-3'-yl-1,4-benzoquinone (D-1)] were found to be strong inhibitors of the activity of reverse transcriptase from human immunodeficiency virus type-1. Under the reaction conditions employed, the enzyme activity was inhibited by more than 70% in the presence of 10 microM each of these compounds. The mode of inhibition by these compounds was competitive with respect to the template.primer, (rA)n.(dT)12-18, and noncompetitive with respect to the triphosphate substrate, dTTP. The Ki values of HIV-1 reverse transcriptase were determined to be 2.3, 1.5, 0.1 and 0.3 microM for ARQ, B1-4, C1-1 and D-1, respectively.
Aspergillus↗
HIV-1 reverse transcriptase inhibitor from Phyllanthus niruri.
An aqueous extract of Phyllanthus niruri (Euphorbiaceae) inhibited human immunodeficiency virus type-1 reverse transcriptase (HIV-1-RT). The inhibitor against HIV-1-RT in this plant was purified by combination of three column chromatographies, Sephadex LH-20, cellulose, and reverse-phase high-performance liquid chromatography. The inhibitor was then identified by nuclear magnetic resonance (NMR) spectra as repandusinic acid A monosodium salt (RA) which was originally isolated from Mallotus repandus. The 50% inhibitory doses (ID50) of RA on HIV-1-RT and DNA polymerase alpha (from HeLa cells) were 0.05 microM and 0.6 microM, respectively, representing approximately a 10-fold more sensitivity of HIV-1-RT compared with DNA polymerase alpha. RA was shown to be a competitive inhibitor with respect to the template-primer while it was a noncompetitive inhibitor with respect to the substrate. RA as low as 10.1 microM inhibited HIV-1-induced cytopathogenicity in MT-4 cells. In addition, 4.5 microM of RA inhibited HIV-1-induced giant cell formation of SUP-T1 approximately 50%. RA (2.5 microM) inhibited up to 90% of HIV-1 specific p24 antigen production in a Clone H9 cell system.
Antigens, Viral↗