Abstract: This disclosure provides a method of treating a subject infected with a mycobacteria of the M. tuberculosis complex or infected with an atypical mycobacterium. Aspects of the method include administering to a subject in need thereof a therapeutically effective amount of an enantiomerically pure (R)-chloroquine agent. The (R)-chloroquine agent may be an analog or derivate of chloroquine having a particular stereochemistry at the position located alpha to the amino-quinoline core of the chloroquine agent. Also provided are methods of inhibiting mycobacteria of the M. tuberculosis complex or other atypical mycobacteria in a cell. Kits and pharmaceutical compositions for practicing the subject methods are also provided.