The completion of the genome of pathogens and the human has provided data that can be utilized to design vaccines and drug targets. One of the recently adopted strategies for drug designing is based on comparative genomics approach, it gives a set of genes that are likely to be essential to the pathogen but absent in the host. By performing homology searches and structural modeling, we can determine which of these proteins can provide novel targets for designing functional inhibitor compounds active against bacteria. In this study, we used three proteins that are potential target, (NCBI Accession no.) NP_216679, NP_218309, NP_218312, for Mycobacterium tuberculosis. Physico-chemical characterization, prediction of secondary structure, disulfide bridges and functional characterization was done to interpret their properties. Three dimensional structure of these proteins were not available as yet at PDB. Therefore, homology models for these proteins were developed using Swiss model server, Modeller and ESyPred3D Web Server. The models were validated using PROCHECK. The study proved that NP_218312 was most stable structure and has good stereo chemical properties. Thus it is selected for further Docking study with antimicrobial peptide, aurein 1.2 and with available drug such as Pyrazinamide, Ethambutol and Isoniazid using HEX. Among these Aurein1.2 was found more effective than other drug, indicates this can be used for further drug designing for Mycobacterium tuberculosis.