). Here we demonstrate that amiloride and EIPA inhibit the enzymatic activity of CVB3 3D pol in vitro, affecting both VPg uridylylation and RNA elongation. Examination of the mechanism of inhibition of 3D pol by amiloride showed that the compound acts as a competitive inhibitor, competing with incoming nucleoside triphosphates (NTPs) and Mg 2؉ . Docking analysis suggested a binding site for amiloride and EIPA in 3D pol , located in close proximity to one of the Mg 2؉ ions and overlapping the nucleotide binding site, thus explaining the observed competition. This is the first report of a molecular mechanism of action of nonnucleoside inhibitors against a picornaviral RNA-dependent RNA polymerase.The family Picornaviridae is a family of positive-sense RNA viruses which contains numerous human pathogens, causing poliomyelitis, myocarditis, meningitis, hepatitis, the common cold, and other diseases. The viral genomic RNA is ϳ7,500 nucleotides (nt) long and contains a 22-amino-acid peptide, VPg, covalently linked to the 5Ј end and a poly(A) tail at the 3Ј end. Genome replication occurs via synthesis of a complementary, negative-sense RNA strand, catalyzed by the viral RNA-dependent RNA polymerase, 3D pol , in association with a number of viral and host proteins. It is a complex process taking place in membrane-associated replication complexes in the cytoplasm of infected cells (reviewed in references 5, 7, and 23). The synthesis of both complementary and genomic RNA strands is initiated by attachment of two UMP nucleotides to a tyrosine residue of VPg, resulting in the production of VPgpUpU. VPg uridylylation requires a template. In the case of genomic strand synthesis, an internal stem-loop in the genomic RNA strand (cis-acting replication element [CRE]) is used as a template, with subsequent translocation of VPg-pUpU to the 3Ј end of the complementary strand and its elongation into a full-length genomic strand (9,15,16,26). The complementary strand synthesis does not absolutely depend on CRE-it can also be templated by the poly(A) tail of the genomic strand (9,15,16,26).VPg uridylylation and RNA elongation have been reproduced successfully in vitro by use of purified components. VPg uridylylation assays require 3D pol , VPg, CRE or poly(A), UTP, and Mg 2ϩ or Mn 2ϩ (19,20), with CRE-templated reaction stimulated by viral proteins 3CD or 3C (18, 19), whereas an elongation assay mix contains an RNA primer instead of VPg (21).Coxsackievirus B3 (CVB3) is a picornavirus responsible for 14 to 32% of human myocarditis cases (1). Amiloride and its derivative 5-(N-ethyl-N-isopropyl)amiloride (EIPA) inhibit CVB3 propagation in cell culture by inhibiting viral genome replication (11). Two amino acid substitutions in 3D pol (S299T and A372V) confer partial resistance of the virus to the compounds, suggesting that amiloride analogues may act as inhibitors of CVB3 3D pol (11). Here we show that amiloride and EIPA inhibit VPg uridylylation and RNA elongation by CVB3 3D pol in vitro, acting as competitive inhibitors with respect to...