Related Experiment Video
Updated: Sep 21, 2026
Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
Published on: April 26, 2024
Computational Modeling and MM-PBSA-Based Molecular Dynamics Investigation of Unexplored tRNA Isoleucine Lysidine
Priyanka Nath1, Bipasha Choudhury2, Saquib Ahmed M A Peerzade3
1MIT ADT School of Bioengineering Sciences and Research, MIT Art, Design and Technology University, Pune, Maharashtra, India. priyanka.nath@mituniversity.edu.in.
Context:
Integrated in-silico approach employed to characterize tRNA isoleucine lysidine synthetase enzyme (MtTilS; UniProt P9WG52), which is essential for protein synthesis in Mycobacterium tuberculosis and to design Amoxicilloyl-Poly-L-Lysine (APL) compounds as putative inhibitors. MtTilS (323 aa) contained TilS (9-230), substrate-binding (249-323) domains and conserved SGGXDS motif. Homology modeling revealed Rossmann-like α/β/α fold, favourable validation (ERRAT 96%, VERIFY3D 81.8%, ProSA - 9.96) and positively charged N-terminal groove (druggability ~ 0.8). APL compounds showed predicted antibacterial activity, high aqueous solubility and low predicted toxicity. Docking prioritized APL-3 (- 7.0 kcal/mol) as favourable inhibitor. Three independent 200 ns molecular dynamics simulations showed preservation of protein fold and ligand association. Cluster analysis indicated convergence toward dominant conformational states. Principal component analysis (PCA) showed broader but reproducible conformational sampling. Free energy landscape (FEL) analysis identified low-energy conformational basins. Dynamic cross-correlation matrix (DCCM) analysis showed conserved correlated residue motions. MM-PBSA indicated favourable binding free energy (-60.0 ± 24.6 kJ/mol) with van der Waals and electrostatic interactions as major contributors while Arg101, Met145, Tyr105, Arg146, Arg140 and Arg219 as major energetic contributors. Preliminary computational evidence supporting MtTilS as target and APL-3 as putative inhibitor candidate necessitating further experimental validation.
Methods:
MtTilS sequence analyzed using CDD, BLAST and MEGA-X. Structure modeled with Phyre2 minimized using Swiss-PDB Viewer/GROMOS96, validated with SAVES-6.0 and visualized in PyMOL-2.0. Binding pockets and druggability predicted using HDOCK and DoGSiteScorer. APL designed in Avogadro (MMFF94) and screened using AntiBac-Pred. ADME/toxicity assessed using SwissADME and ProTox-II. Docking performed with AutoDock Vina-1.2.0 and MD using GROMACS (CHARMM36ff). Trajectories analyzed by PCA, FEL, DCCM and MM/PBSA.
