Rupintrivir (formerly AG7088) is an irreversible inhibitor of the human rhinovirus (HRV) 3C protease that has been demonstrated to have in vitro activity against all HRVs tested, consistent with its interaction with a strictly conserved subset of amino acids in the 3C protease. The potential for resistance was studied following in vitro serial passage of HRV serotypes 14, 2, 39, and Hanks in the presence of increasing rupintrivir concentrations. HRV variants with reduced susceptibilities to rupintrivir (sevenfold for HRV 14) or with no significant reductions in susceptibility but genotypic changes (HRV 2, 39, and Hanks) were initially isolated following 14 to 40 cumulative days in culture (three to six passages). Sequence analysis of the 3C protease identified one to three substitutions in diverse patterns but with common features (T129T/A, T131T/A, and T143P/S in HRV 14; N165T in HRV 2; N130N/K and L136L/F in HRV 39; T130A in HRV Hanks). Notably, three of the four HRV variants contained a substitution at residue 130 (residue 129 in HRV 14). Continued selection in the presence of escalating concentrations of rupintrivir (40 to 72 days) resulted in the accumulation of additional mutations (A121A/V and Y139Y/H in HRV 14, E3E/G and A103A/V in HRV 2, S105T in HRV 39), with only minimal further reductions in susceptibility (up to fivefold). The ability of specific substitutions to confer resistance was examined by susceptibility testing of HRV 14 variants constructed to contain 3C protease mutations. In summary, the slow accumulation of multiple amino acid substitutions with only minimal to moderate reductions in susceptibility highlight the advantages of 3C protease as an antiviral target.Human rhinoviruses (HRVs), which are members of the family Picornaviridae, comprise over 100 different serotypes and are the predominant cause of the common cold. Although HRV infections are generally mild and self-limiting, they can also be associated with more serious illnesses, specifically, exacerbation of disease in individuals with underlying respiratory disorders (1,2,3,5,6,18,26,29). Although no effective antiviral therapies have been approved for the treatment of HRV infections, chemotherapeutic approaches that utilize antiviral agents directed toward viral attachment, capsid uncoating, and 3C protease have been well studied (reviewed in reference 22). Our research efforts have focused on the inhibition of the picornavirus 3C protease, an enzyme absolutely required for viral replication (15,21).Rupintrivir (formerly AG7088) is a novel, irreversible inhibitor of 3C protease that was discovered by using structure-based drug design methodologies and was formulated for intranasal delivery in human clinical trials (8-11, 13, 19). Parallel efforts to identify a 3C protease inhibitor that was orally bioavailable led to the discovery of compound 1 (7, 24). Similar to rupintrivir, compound 1 is an irreversible inhibitor that incorporates a Michael acceptor moiety that forms a covalent bond with the 3C protease active-site cysteine ...