Human immunodeficiency virus reverse transcriptase: steady-state and pre-steady-state kinetics of nucleotide incorporation

Kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204E

The bis(heteroaryl)piperazine U-88204E is a potent inhibitor of HIV-1 reverse transcriptase (RT) and possesses excellent anti-HIV activity in HIV-1-infected lymphocytes grown in tissue culture. Enzymatic kinetic studies of the RNA- and DNA-dependent DNA polymerases of RT were carried out in order to determine whether the inhibitor interacts directly with the template:primer or deoxyribonucleotide triphosphate (dNTP) binding sites of the polymerase. The experimental results were analyzed using steady-state or Briggs-Haldane kinetics, by assuming that the template:primer binds to the enzyme first followed by the dNTP and that the polymerase functions processively. The results of the analysis show that the inhibitor acts as a mixed to noncompetitive inhibitor with respect to both the template:primer and the dNTP binding sites. The potency of U-88204E on the RNA-directed DNA polymerase activity depends on the base composition of the template:primer. The Ki values for the poly(rC):(dG)10-directed reactions were at least 7 times lower than the ones for reactions directed by poly(rA):(dT)10. The inhibitor did not inhibit the RNase H function of HIV-1 RT nor did it impair the RNA-directed DNA polymerase activity of HIV-2 RT. These data thus demonstrate the unique specificity of U-88204E for HIV-1 RT.

Mechanism of resistance of human immunodeficiency virus type 1 to 2',3'-dideoxyinosine

A molecular clone containing the wild-type reverse transcriptase (RT) coding region of human immunodeficiency virus type 1 (HIV-1) was constructed, and site-directed mutagenesis was used to introduce mutations--Leu74-->Val (L74V), T215Y, and the combination L74V/T215Y--into the RT coding region. The proteins were purified by immunoaffinity chromatography. Assays were performed with mutant and wild-type RT to determine substrate and inhibitor specificity. All three mutant enzymes catalyzed the incorporation of substrate 2'-deoxynucleoside 5'-triphosphates (dNTPs) as efficiently as wild-type HIV-1 RT. Small changes were observed in the Km values for dNTPs with all three mutant enzymes, while more significant changes were noted in sensitivity to nucleoside 5'-triphosphate analogues that inhibit the enzyme activity. Results suggest that altered substrate recognition by the HIV-1 RT is involved in the mechanism of resistance.

Rapid kinetic analysis of a point mutant of HIV-1 reverse transcriptase lacking ribonuclease H activity

The comparative kinetics of RNA-dependent DNA polymerization catalyzed by wild-type HIV-1 reverse transcriptase and a point mutant specifically lacking RNase H activity were analyzed using a heteropolymeric substrate consisting of a 19-mer primer hybridized to a 345-nucleotide RNA template. The rapid-quench product distributions generated under single-turnover conditions, in which primer extension by the two enzymes was restricted to the incorporation of 5 nucleotides (N+5), were significantly different. Whereas the wild-type enzyme catalyzed synthesis of the N+5 product over the time course of the reaction (20 ms-10 s) with a relatively low degree of processivity, the extent of accumulation of the intermediate N+2 and N+3 products was grossly exaggerated in the parallel mutant-catalyzed time course. The observation of concomitant polymerase-dependent hydrolysis during the course of synthesis catalyzed by the wild-type enzyme suggested that the inability of the RNase H- mutant to hydrolyze the RNA template created blocks to further synthesis by reducing the rates of DNA polymerization at these intermediate positions, and hence impaired the ability of this mutant to complete cDNA synthesis.

Mechanism of DNA strand transfer reactions catalyzed by HIV-1 reverse transcriptase

Two DNA strand transfer reactions occur during retroviral reverse transcription. The mechanism of the first, minus strand strong-stop DNA, transfer has been studied in vitro with human immunodeficiency virus 1 reverse transcriptase (HIV-1 RT) and a model template-primer system derived from the HIV-1 genome. The results reveal that HIV-1 RT alone can catalyze DNA strand transfer reactions. Two kinetically distinct ribonuclease (RNase) H activities associated with HIV-1 RT are required for removal of RNA fragments annealed to the nascent DNA strand. Examination of the binding of DNA.RNA duplex and single-stranded RNA to HIV-1 RT during strand transfer supports a model where the enzyme accommodates both the acceptor RNA template and the nascent DNA strand before the transfer event is completed. The polymerase activity incorporated additional bases beyond the 5' end of the RNA template, resulting in a base misincorporation upon DNA strand transfer. Such a process occurring in vivo during retroviral homologous recombination could contribute to the hypermutability of the HIV-1 genome.