Inhibition of HIV-1 integrase by modified oligonucleotides derived from U5' LTR

Retroviral integrase catalyzes integration of double-stranded viral DNA int o the host chromosome by a process that has become an attractive target for drug design. In the 3' processing reaction, two nucleotides are specifical ly cleaved from both 3' ends of viral DNA yielding a 5' phosphorylated dime r (pGT). The resulting recessed 3' hydroxy groups of adenosine provide the attachment sites to the host DNA in the strand transfer reaction. Here, we studied the effect of modified double-stranded oligonucleotides mimicking b oth the unprocessed (21-mer oligonucleotides) and 3' processed (19-mer olig onucleotides) U5 termini of proviral DNA on activities of HIV-1 integrase i n vitro. The inhibitions of 3' processing and strand transfer reactions wer e studied using 21-mer oligonucleotides containing isopolar, nonisosteric, both conformationally flexible and restricted phosphonate inter-nucleotide linkages between the conservative AG of the sequence CAGT, and using a 21-m er oligonucleotide containing 2'-fluoroarabinofuranosyladenine. All modifie d 21-mer oligonucleotides competitively inhibited both reactions mediated b y HIV-1 integrase with nanomolar IC50 values. Our studies with 19-mer oligo nucleotides showed that modifications of the 3' hydroxyl significantly redu ced the strand transfer reaction. The inhibition of integrase with 19-mer o ligonucleotides terminated by (S)-9-(3-hydroxy-2-phosphonomethoxypropyl)ade nine, 9-(2-phosphonomethoxyethyl)adenine, and adenosine showed that proper orientation of the 3' OH group and the presence of the furanose ring of ade nosine significantly influence the strand transfer reaction.