Drugs are small organic molecules compared to their binding target. They stimulate or inhibit the action of biomolecules, like proteins, providing therapeutic benefits. Drug design is the process of developing novel drugs based on understanding biological targets. It is an expensive and time-consuming process. Tuberculosis is a contagious bacterial illness marked by the development of small growths (tubercles) in the body tissues, particularly the lungs. The current investigation indicates that pantothenate synthetase is a promising focus for developing drugs to treat tuberculosis. Pantothenate synthetase is an enzyme that plays a role in fatty acid synthesis in Mycobacterium tuberculosis (Mtb). 6H-Indolo[2,3-b] quinoxaline is a heterocyclic compound found to be a potential lead for anti-tubercular drug design. Selection of the lead molecule based on virtual screening using iGEMDOCK v.2 software. Sixteen 6H-Indolo[2,3-b] quinoxaline derivatives were selected according to Lipinski’s rule of five and by evaluating the parameters. All the derivatives were docked on the enzyme Mtb Pantothenate synthetase (pdb accession code: 3IMG). All the ligands interact well with the key binding sites GLY 153 and ALA 181. The results showed that the ligands of binding energies in the range of-4.91kcal/mol and -8.06 kcal/mol with Mtb Pantothenate synthetase, indicating that the compounds possess good binding with the active sites and inhibit the enzyme quite prominently. When compared with the standard drug Isoniazid, compounds ISA 2, ISA 5 and ISA 6 of the first series and ISB 1, ISB 2 and ISB 6 of the second series exhibited high binding energy towards 3IMG