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MOLECULAR PHARMACOLOGY 51:567-575 (1997).

Probing Interactions between Viral DNA and Human Immunodeficiency Virus Type 1 Integrase Using Dinucleotides

Abhijit Mazumder, Hiroyuki Uchida, Nouri Neamati, Sanjay Sunder, Maria Jaworska-Maslanka, Eric Wickstrom, Fan Zeng, Roger A. Jones, Robert F. Mandes, H. Keith Chenault, and Yves Pommier

Laboratories of Molecular Pharmacology, Division of Basic Sciences (A.M., N.N., S.S., Y.P.), and Experimental Retrovirology Section (H.U.), Medicine Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, Department of Pharmacology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107-5541 (M.J.-M., E.W.), Department of Chemistry, Rutgers State University of New Jersey, Piscataway, New Jersey 08855-0939 (F.Z., R.A.J.), and Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716 (R.F.M., H.K.C.)

Retroviral integrases are essential for viral replication and represent an attractive chemotherapeutic target. In the current study, we demonstrated the activity of micromolar concentrations of dinucleotides against human immunodeficiency virus type 1 (HIV-1), HIV type 2 (HIV-2), simian immunodeficiency virus, and feline immunodeficiency virus integrases. The structure-activity relationship indicates that 5-phosphorylation enhances potency and that phosphodiester and sugar modifications affect the inhibition of HIV-1 integrase. Base sequence selectivity was observed: pAC, pAT, and pCT were the most potent inhibitors, whereas pAA, pGA, and pGC showed low activity at 100 µM. The inhibition by pAC is consistent with the interaction of the enzyme with the 5 end of the noncleaved strand (5-AC-3). The linear and cyclic dinucleotides released by the 3-processing reaction did not affect enzymatic activity at physiological concentrations. An increase in the length to trinucleotides or tetranucleotides enhanced potency by only 2-3-fold, suggesting that two neighboring bases may be sufficient for significant interactions. Inhibition of a truncated (50-212) integrase mutant and global inhibition of all nucleophiles in the 3-processing reaction suggest that dinucleotides bind in the catalytic core. All of the active dinucleotides inhibited enzyme/DNA binding in their respective IC₅₀ range. Although the dinucleotides tested showed no antiviral activity, these observations demonstrate the usefulness of dinucleotides in elucidating enzyme mechanisms and as potential ligands for cocrystallization and as lead structures for development of antivirals.