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An approach for inhibiting the ribonuclease H (RNase H) activity of human immunodeficiency virus type I (HIV-I) reverse transcriptase (RT) is demonstrated by targeting RNase H RNA.DNA hybrid substrates. In this approach the binding of the 4,5-disubstituted 2-deoxystreptamine aminoglycosides, neomycin, paromomycin and ribostamycin, to two different chimeric RNA-DNA duplexes inhibits specific RT-mediated RNase cleavage in competitive manner.

Spectroscopic and calorimetric technique were employed to characterize and contrast the binding of the aminoglycoside paromomycin to three octamer nucleic acid duplexes of identical sequence but different strand composition .The structures and stabilities of DNA.RNA hybrid duplexes can vary considerably with the sequence composition of DNA and RNA strands. Reverse transcriptase -mediated Rnase H processing of DNA.RNA hybrid domains is essential for the replication of retroviruses.

RNA degradation via the ribonuclease H (RNase H) activity of human immunodeficiency virus type I (HIV-1) reverse transcriptase (RT) is a critical component of the reverse transcription process. In this connection, mutations of RT that inactivate RNase H activity result in noninfectious virus particles. Thus, interfering with the RNase H activity of RT represents a potential vehicle for the inhibition of HIV-1 replication. Here, we demonstrate an approach for inhibiting the RNase H activity of HIV-1 RT by targeting its RNADNA hybrid substrates. Specifically, we show that the binding of the 4,5-disubstituted 2-deoxystreptamine aminoglycosides, neomycin, paromomycin, and ribostamycin, to two different chimeric RNA-DNA duplexes, which mimic two distinct intermediates in the reverse transcription process, inhibits specific RT-mediated RNase H cleavage, with this inhibition being competitive in nature. UV melting and isothermal titration calorimetry studies reveal a correlation between the relative binding affinities of the three drugs for each of the chimeric RNA-DNA host duplexes and the relative extents to which the drugs inhibit RT-mediated RNase H cleavage of the duplexes. Significantly, this correlation also extends to the relative efficacies with which the drugs inhibit HIV- 1 replication. In the aggregate, our results highlight a potential strategy for AIDS chemotherapy that should not be compromised by the unusual genetic diversity of HIV- 1. [ABSTRACT FROM AUTHOR]

Employs a broad range of biophysical, biochemical and computer modeling techniques to characterize and cross-correlate the DNA-binding and topoisomerase poisoning properties of four protoberberine analogues. Consistency of results with a mechanistic model in which both ligand-DNA and ligand-enzyme interactions are important for the poisoning of topoisomerase I.