Enzymatic Post-Transfer Editing Mechanism of E. coli Threonyl-tRNA Synthetase (ThrRS): A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Investigation

Palladium(ii), platinum(ii), and silver(i) complexes with 3-acetylcoumarin benzoylhydrazone Schiff base: Synthesis, characterization, biomolecular interactions, cytotoxic activity, and computational studies

New Pd(ii) (C1), Pt(ii) (C2), and Ag(i) (C3) complexes derived from 3-acetylcoumarin benzoylhydrazone (HL) Schiff base were synthesized and characterized by FTIR, 1H NMR, UV-visible spectroscopies along with elemental analysis (C, H, N), magnetic, molar conductivity measurements, and DFT calculations. The obtained results suggested that the ligand had different behaviors in the complexes: mono-negative tridentate (C1) and neutral tridentate (C2) as an ONO-donor and neutral bidentate (C3) as an ON-donor. Quantum chemistry calculations were performed to validate the stability of the suggested geometries and indicated that all the complexes possess tetra-coordinated metal ions. The binding affinity of all the compounds toward calf thymus (ctDNA), yeast (tRNA), and bovine serum albumin (BSA) was evaluated by absorption/emission spectral titration studies, which revealed the intercalative binding to ctDNA and tRNA and static binding upon complex formation with BSA. Molecular insights into the binding affinity of the characterized complexes were provided through conducting molecular docking analysis. Moreover, the cytotoxic activity (in vitro) of the compounds was screened against human cancerous cell lines and a non-cancerous lung fibroblast (WI38) one using cis-platin as a reference drug. The IC50 and selective index (SI) values indicated the higher cytotoxic activity of all the metal complexes compared to their parent ligand. Among all the compounds, the complex C2 showed the highest activity. These results confirmed the improvement of the anticancer activity of the ligand by incorporating the metal ions. In addition, flow cytometry results showed that complexes C1 and C2 induced cell cycle arrest at S and G1/S, respectively.

QM/MM investigation of the discriminatory pre-transfer editing mechanism operated by Lysyl-tRNA synthetase

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that remarkable facilitate the aminoacylation process during translation. With a high fidelity, the mischarged tRNA is prevented through implementing pre- and post-transfer proofreading mechanisms. For instance, Lysine-tRNA synthetase charges the native substrate, lysine, to its cognate tRNA. In spite of the great structural similarity between lysine to the noncognate and toxic ornithine, with the side chain of lysine being only one methylene group longer, LysRS is able to achieve this discrimination with a high efficiency. In this work, the hybrid quantum mechanics/molecular mechanics (QM/MM) investigation was applied to probe the pre-transfer editing mechanism catalyzed by lysyl-tRNA synthetase to reject the noncognte aminoacyl, L-ornityl (Orn), compared to the cognate substrate, L-lysyl. Particularly, the self-cyclization pre-transfer editing mechanism was explored for the two substrates. The substrate-assisted self-cyclization editing of Orn-AMP, where its phosphate moiety acts as the catalytic base, is found to be the rate-determining step with an energy barrier of 101.2 kJ mol-1. Meanwhile, the corresponding rate-limiting pathway for the native Lys-AMP lies at 140.2 kJ mol-1. This observation clearly indicated the infeasibility of this catalytic scenario in the presence of the native substrate. Interestingly, a thermodynamically favorable cyclic product of -92.9 kJ mol-1 with respect to the aminoacyl reactant complex demonstrated evidence of a successful pre-transfer editing. This reaction resulted in the discharge of the on-cognate -ornithine derivative from LysU's active site. These valuable mechanistic insights are valuable to enrich our knowledge of this extremely efficient and specific catalytic machinery of LysRS.Communicated by Ramaswamy H. Sarma.

Screening a library of potential competitive inhibitors against bacterial threonyl-tRNA synthetase: DFT calculations

Due to the growing interest in directing aminoacyl-tRNA synthetases for antimicrobial therapies, evaluating the binding proficiency of potential inhibitors against this target holds significant importance. In this work, we proposed potential ligands that could properly bind to the crucial Zn(II) cofactor located in the active site of Threonyl-tRNA synthetases (ThrRS), potentially functioning as competitive inhibitors. Initially, detailed DFT quantum chemical study was conducted to examine the binding ability of threonine against unnatural amino acids to cofactor Zn(II). Then, the binding energy value for each suggested ligand has been determined and compared to the value determined for the native substrate, threonine. Our screening investigation showed that the native threonine should coordinate in a bidentate fashion to this Zn(II) which lead to the highest (binding energy) BE Thereby, the synthetic site of ThrRS rejects unnatural amino acids that cannot afford this type of coordination to Zn(II) ion which has been supported by our calculations. Moreover, based on their binding to the Zn(II) and the obtained BE values compared to the cognate threonine, many potent ligands have been suggested. Importantly, ligands with deprotonated warheads showed the highest binding ability amongst a list of potential hits. Further investigation on the selected ligands using molecular docking and QM/MM calculations confirmed our findings of the suggested ligands being able to bind efficiently in the active site of ThrRS. The suggested hits from this study should be valuable in paving routs for developing candidates as competitive inhibitors against the bacterial ThrRS.Communicated by Ramaswamy H. Sarma.

Unraveling the Critical Role Played by Ado762'OH in the Post-Transfer Editing by Archaeal Threonyl-tRNA Synthetase

Archaeal threonyl-tRNA synthetase (ThrRS) possesses an editing active site wherein tRNA^Thr that has been misaminoacylated with serine (i.e., Ser-tRNA^Thr) is hydrolytically cleaved to serine and tRNA^Thr. It has been suggested that the free ribose sugar hydroxyl of Ado76 of the tRNA^Thr (_Ado762'OH) is the mechanistic base, promoting hydrolysis by orienting a nucleophilic water near the scissile Ser-tRNA^Thr ester bond. We have performed a computational study, involving molecular dynamics (MD) and hybrid ONIOM quantum mechanics/molecular mechanics (QM/MM) methods, considering all possible editing mechanisms to gain an understanding of the role played by _Ado762'OH group. More specifically, a range of concerted or stepwise mechanisms involving four-, six-, or eight-membered transition structures (total of seven mechanisms) were considered. In addition, these seven mechanisms were fully optimized using three different DFT functionals, namely, B3LYP, M06-2X, and M06-HF. The M06-HF functional gave the most feasible energy barriers followed by the M06-2X functional. The most favorable mechanism proceeds stepwise through two six-membered ring transition states in which the _Ado762'OH group participates, overall, as a shuttle for the proton transfer from the nucleophilic H₂O to the bridging oxygen (_Ado763'O) of the substrate. More specifically, in the first step, which has a barrier of 25.9 kcal/mol, the _Ado762'-OH group accepts a proton from the attacking nucleophilic water while concomitantly transferring its proton onto the substrates C-O_carb center. Then, in the second step, which also proceeds with a barrier of 25.9 kcal/mol, the _Ado762'-OH group transfers its proton on the adjacent _Ado763'-oxygen, cleaving the scissile C_carb-O3'_Ado76 bond, while concomitantly accepting a proton from the previously formed C-O_carbH group.

Protonation state and fine structure of the active site determine the reactivity of dehydratase: hydration and isomerization of β-myrcene catalyzed by linalool dehydratase/isomerase from Castellaniella defragrans

Linalool dehydratase/isomerase (LinD) from Castellaniella defragrans is a bifunctional enzyme that catalyzes the hydration of β-myrcene to (S)-linalool and isomerization of (S)-linalool to geraniol.