## 3 Results
### MM/PBSA-Based Interaction Energy Calculation  
The computational efficiency and accuracy of simulation-based end point methods such as molecular mechanics with Poisson-Boltzmann (MM/PBSA) and molecular mechanics with generalized Born and surface area (MM/GBSA) provides a reliable choice for binding free energy calculations [42]. These methods are based upon sampling of the final state of the system and the solvent is treated implicitly, thus reducing the computational time. However, these methods possess limitations regarding the estimation of conformational and solvation entropies [48]. In order to prioritize and re-rank the compounds, MM/PBSA-based binding free energy was calculated for all the nine complexes. For each system, 100 snapshots were fetched at the interval of 50 ps along the last five ns trajectory. All the compounds showed favorable binding free energy values. The compound BTB14738 was predicted to show the highest binding free energy value of \(-\)72.27 \(\pm\) 12.63 KJ/mol. The other compounds RH00608, SPB02705, CD01000, and HTS07760 are also predicted to show high binding free energy values of \(-\)68.06 \(\pm\) 11.80, \(-\)63.57 \(\pm\) 12.22, \(-\)51.28 \(\pm\) 13.74, and \(-\)53.17 \(\pm\) 12.68 KJ/mol. However, the compound SEW02765 is predicted to show the lowest binding free energy value. The binding free energies of protein-ligand complexes is summarized in Table 2. The compounds were ranked upon the basis of predicted binding free energy. The selected compounds showed high predicted binding free energy, indicating better binding and potentially better inhibitory efficiency. The MM/PBSA approach has been reported to be applied reliably for re-scoring the protein-ligand complexes predicted by molecular docking. Thus, it helps in boosting the virtual screening hit rates [31; 49]. The accuracy of the method is limited by the lack of conformational entropy, missing effect of water molecules in the binding site and details in the method, such as dielectric constant, continuum-solvation method, and charges [50]. Therefore, this method has been applied to systems with a varying degree of success. Nevertheless, the method has been useful to corroborate the docking results and understand the observed affinities [51; 52].  
Taking into consideration the predicted binding free energy values, stability of the bound ligand along with molecular docking score, four compounds (BTB14738, SPB02705, RH00608, and CD01000) were selected as potential hits (Figure 3). For compound BTB14738, the highest binding free energy of \(-\)72.27 \(\pm\) 12.63 was estimated. The ligand r.m.s.d was calculated to be 0.11 nm, indicating high stability. Similarly, the compounds RH00608, SPB02705, and CD01000 also showed high favorable binding free energy values and stable ligand binding. Thus, molecular docking-based virtual screening together with molecular dynamics and the MM/PBSA method has resulted in the identification of pioneer putative hits against Mtb FAS-I.  
\begin{table}
\begin{tabular}{c c c c} \hline \hline
**Serial Number** & **Compound ID** & \
\begin{tabular}{c} **Predicted Binding** \\ **Free Energy (KJ/mol)** \\ \end{tabular} &
\begin{tabular}{c} **Molecular Docking** \\ **Score** \\ \end{tabular} \\ \hline
1. & BTB14738 & \(-\)72.27 \(\pm\) 12.63 & 9.55 \\ \hline
2. & RH00608 & \(-\)68.06 \(\pm\) 11.80 & 10.80 \\ \hline
3. & SPB02705 & \(-\)63.57 \(\pm\) 12.22 & 9.30 \\ \hline
4. & HTS07760 & \(-\)53.17 \(\pm\) 12.68 & 9.28 \\ \hline
5. & CD01000 & \(-\)51.28 \(\pm\) 13.74 & 10.41 \\ \hline
6. & BTB14516 & \(-\)48.91 \(\pm\) 11.37 & 10.01 \\ \hline
7. & RJF01717 & \(-\)44.82 \(\pm\) 15.77 & 10.18 \\ \hline
8. & HTS09453 & \(-\)43.30 \(\pm\) 14.27 & 10.46 \\ \hline
9. & SEW02765 & \(-\)16.44 \(\pm\) 13.22 & 9.75 \\ \hline \hline \end{tabular}
\end{table}
Table 2: The predicted binding free energy and molecular docking score for selected protein-ligand complexes is listed.