3D QSAR, Docking, Molecular Dynamics Simulations and MM-GBSA studies of Extended Side Chain of the Antitubercular Drug (6S) 2-Nitro-6- {[4-(trifluoromethoxy) benzyl] oxy}-6,7-dihydro-5H-imidazo[2,1-b] [1,3] oxazine.

Background: PA-824 analogues have been proposed on a promising approach for treating MDR/XDR tuberculosis. In order to understand the structural requirement of reported extended side chain analogues were studied to get insight into their structural requirements responsible for high affinity as a ligand-based pharmacophore, 3D-QSAR model have been developed. Docking and molecular dynamics studies revealed the better binding interaction of inhibitor binding pocket of deazaflavin dependent nitroreductase (Ddn) with cofactor F420 crystal. Methods: For pharmacophore generation and atom-based 3D-QSAR analysis, a dataset of 84 compounds were selected which were carried out using PHASE. The docking studies were performed using Glide module consists of five steps protein preparation, ligand preparation, receptor grid generation, actual docking procedure and finally viewing the docking results using the poseviewer. QikProp provides ranges for comparing a particular molecule’s properties with those of 95% of known drugs. Molecular dynamics (MD) simulations for docking complex of deazaflavin dependent nitroreductase (Ddn) with molecule 63 were performed using Desmond. Prime Molecular Mechanics/Generalized-Born/Surface Area (MM-GBSA) was used for the calculation of binding free energy for the docked complexes. Results: The pharmacophore hypothesis yielded a statistically significant 3D-QSAR model, with a correlation coefficient of R2 = 0.8988 for training set compounds, higher variance ratio F= 127.3 and the model generated showed excellent predictive power, with a correlation coefficient of structure to analyses Q2= 0.8543 for a randomly chosen test set of 17 compounds. The binding position of most active molecule 63 is shown in figure 4. Several favorable interactions between ligand and enzyme clearly observed; H-bond showed between O atom presence as spacer in C-6- 2-Nitro-6-[4-(trifluoromethoxy) benzyl] oxy-6,7-dihydro-5H-imidazo[2,1-b] [1,3] oxazine and Asn 62. Weak hydrogen bonding observed between N1 atom in imidazole ring and Asn91. The binding of imidazole nucleus occurs at site, which has extensive hydrophobic interaction with Arg60 residues. All these pharmacokinetic parameters within the acceptable range defined for human use, thereby indicating their potential as drug- like molecule. Stability of deazaflavin dependent nitroreductase (Ddn) with molecule 63 complex was evaluated through 100 ns molecular dynamic simulations. Main contributions to the tight binding of molecule 63 to Ddn are the exceptionally electrostatics (dG_bind_Coulomb) and enhance hydrogen bond interactions (dG_bind_Hbond). Conclusion: Docking, MM-GBSA, MD stimulation, pharmacophore model and 3D-QSAR studies as well as QikProp pharmacokinetic analysis presented in this paper is hoped to be a primer towards the development of various novel PA-824 with different chemical scaffolds and further its biological activity predictions to invent novel, potent, selective and safe PA-824 analogues for the treatment of MDR/XDR tuberculosis. Moreover, further use of contemporary experimental and computational techniques to data presented here may widen its scope and applicability.