Visceral leishmaniasis is a parasitic disease caused by the protozoan scrounger Leishmania donovani. This disease is responsible for high rates of mortality and morbidity, especially in tropical regions of the world including India. With increasing problems due to resistance and clinical efficacy, the drugs currently used to treat this disease is becoming increasingly less effective, resulting in the urgent need for finding novel drug targets and new drug candidates in this area. Presented study describes comparative metabolomic approach through which entire metabolomes of Homo sapiens and Leishmania major are compared to detect unique biochemical reactions in them and further analysis of developing a structural model for enzyme holding key position in parasite?s metabolic network using homology modeling approach. Here we report 97 potential target proteins and molecular structure of one target (Trypanothione reductase) from two subspecies (Leishmania donovani and Leishmania major) is described and compared. Results from current study can be used as background for developing new drug candidates against novel drug target described herein.