Abstract:JC polyomavirus (JCPyV) is a common human pathogen that results in a chronic asymptomatic infection in healthy adults. Under conditions of immunosuppression, JCPyV spreads to the central nervous system and can cause the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML), a disease for which there are no vaccines or antiviral therapies. Retro‐2 is a previously identified small molecule inhibitor that was originally shown to block retrograde transport of toxins such as ricin toxin from endosomes to the Golgi apparatus and endoplasmic reticulum (ER), and Retro‐2.1 is a chemical analog of Retro‐2 that has been shown to inhibit ricin intoxication of cells at low nanomolar concentrations. Retro‐2 has previously been shown to prevent retrograde transport of JCPyV virions to the ER, but the effect of Retro‐2.1 on JCPyV infectivity is unknown. Here it is shown that Retro‐2.1 inhibits JCPyV with an EC50 of 3.9 μM. This molecule inhibits JCPyV infection at dosages that are not toxic to human tissue culture cells. Retro‐2.1 was also tested against two other polyomaviruses, the human BK polyomavirus and simian virus 40, and was also shown to inhibit infection at similar concentrations. Viral uncoating studies demonstrate that Retro‐2.1 inhibits BKPyV infectivity in a manner similar to Retro‐2. These studies demonstrate that improved analogs of Retro‐2 can inhibit infection at lower dosages than Retro‐2 and further optimization of these compounds may lead to effective treatment options for those suffering from JCPyV infection and PML.