Amino Acid Specificity of Ancestral Aminoacyl-tRNA Synthetase Prior to the Last Universal Common Ancestor Commonote commonote

Development of potent inhibitors targeting bacterial prolyl-tRNA synthetase through fluorine scanning-directed activity tuning

As essential enzymes encoded by single genes, aminoacyl-tRNA synthetases (aaRSs) have long been considered promising drug targets for combating microbial infections. In this study, we developed a novel class of amino acid-ATP dual-site inhibitors of prolyl-tRNA synthetase (ProRS) through the structural simplification of the intermediate product prolyl adenylate and its non-hydrolyzable mimic. The co-crystal structures of the compound PAA-5 bound to both Pseudomonas aeruginosa and human cytoplasmic ProRSs (PaProRS and HsPrors) were solved to high resolution. Utilizing the structural information gained, a fluorine scanning (F-scanning) strategy was applied to PAA-5, and the biochemical and biophysical assays demonstrated that fluorine substitutions at specific positions of PAA-5 selectively enhanced its activity against bacterial ProRS. The dual-fluorinated derivative PAA-38 exhibited the highest antibacterial potency, with a Kd value of 0.399 ± 0.074 nM and an IC50 value of 4.97 ± 0.98 nM against PaProRS and an MIC value of 4-8 μg mL-1 against tested bacterial strains. Our study provides a novel lead compound for the development of aaRS-based antibiotics and highlights F-scanning as a powerful strategy for lead optimization, particularly in pinpointing the subtle fluorophilic environments within the protein pocket to achieve better activity and selectivity.

Unveiling Highly Active and Stable l-Glutaminase through Ancestral Sequence Reconstruction and Turnover Number Prediction

In our study, we employed ancestral sequence reconstruction and DLKcat analysis to engineer l-glutaminases with enhanced activity and thermal stability, using Bacillus subtilis 168 l-glutaminase (YbgJ) as the template. We identified two ancestral l-glutaminases, Anc165 and Anc194, with specific activities 730.6- and 203.5-fold higher than YbgJ, respectively. Anc165 retained 96% activity at 65 °C and 69% at 70 °C for 30 min, while Anc194 maintained over 40% activity at 70 °C, contrasting with YbgJ, which was inactivated above 55 °C. In a 15% NaCl solution, Anc165 and Anc194 retained 100 and 18% activity, respectively, compared to YbgJ's complete loss. Molecular dynamics simulations indicate that the enhanced thermal stability of Anc165 is due to its increased structural rigidity. The enhanced activity of Anc165 is due to a more stable enzyme-substrate complex with l-glutamine. In a simulated soy sauce fermentation system, Anc165 produced about 10% more glutamate than YbgJ. With high-thermal stability and activity, Anc165 could be a potential candidate for industrial applications.