c All currently approved antiviral drugs for the treatment of chronic hepatitis B virus (HBV) infection are nucleos(t)ide reverse transcriptase inhibitors (NRTI), which inhibit the DNA synthesis activity of the HBV polymerase. The polymerase is a unique reverse transcriptase (RT) that has a novel protein priming activity in which HP initiates viral DNA synthesis using itself as a protein primer. We have determined the ability of NRTI-triphosphates (TP) to inhibit HBV protein priming and their mechanisms of action. While entecavir-TP (a dGTP analog) inhibited protein priming initiated specifically with dGTP, clevudine-TP (a TTP analog) was able to inhibit protein priming independently of the deoxynucleoside triphosphate (dNTP) substrate and without being incorporated into DNA. We next investigated the effect of NRTIs on the second stage of protein priming, wherein two dAMP nucleotides are added to the initial deoxyguanosine nucleotide. The obtained results indicated that clevudine-TP as well as tenofovir DF-DP strongly inhibited the second stage of protein priming. Tenofovir DF-DP was incorporated into the viral DNA primer, whereas clevudine-TP inhibited the second stage of priming without being incorporated. Finally, kinetic analyses using the HBV endogenous polymerase assay revealed that clevudine-TP inhibited DNA chain elongation by HP in a noncompetitive manner. Thus, clevudine-TP appears to have the unique ability to inhibit HBV RT via binding to and distorting the HP active site, sharing properties with both NRTIs and nonnucleoside RT inhibitors. C hronic hepatitis B virus (HBV) infection remains a worldwide health problem, afflicting over 350 million patients and resulting in one million deaths per year (1). HBV has a ca. 3.2-kb relaxed circular (RC) DNA genome that is repaired to form a covalently closed circular (CCC) DNA in the host cell. CCC DNA is then transcribed by the host RNA polymerase II to produce a pregenomic RNA (pgRNA), the precursor to RC DNA (2, 3). Reverse transcription of pgRNA by the viral polymerase (HP), a multifunctional reverse transcriptase (RT), generates first the minus strand and then the plus strand of RC DNA using its RNA-and DNA-dependent DNA polymerization activities, respectively (2, 4).Initiation of viral minus-strand DNA synthesis occurs via a novel protein priming mechanism in which HP, specifically a tyrosine residue (Y63) in its N-terminal domain, serves as a protein primer, while its central RT domain serves as the catalyst (5-9). Furthermore, protein-primed initiation of reverse transcription requires a short RNA stem-loop structure, termed epsilon (Hε), on the 5= end of pgRNA, which is recognized specifically by HP in a host chaperone-dependent reaction (7, 10-15). Hε, specifically the last three nucleotides of its internal bulge, serves as the specific template for protein priming (7,10,16). Furthermore, it serves as an allosteric activator of the HP enzymatic activity (17, 18). The product of protein priming is a short, 3-nucleotide (nt)-long (dGAA) viral minus-st...