Methods and compositions for treating disease caused by infectious agents, particularly tuberculosis are provided. In particular, methods and compositions comprising substituted derivatives of capuramycin analogs for the treatment of infectious diseases are provided. Also provided are capuramycin analogue formulations comprising PEGylated compounds, including a PEGylated vitamin E derivative, liposomes and nanoparticle carriers. The invention provides methods and compositions comprising a capuramycin analogue and capuramycin analogues in combination with one or more other active agents.