Design, dynamic docking, synthesis, and <i>in vitro</i> validation of a novel DNA gyrase B inhibitor

Methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and vancomycin-intermediate-resistant <i>Staphylococcus aureus</i> (VRSA) are among the WHO's high priority pathogens. Among these two, MRSA is the most globally documented pathogen that necessitates the pressing demand for new classes of anti-MRSA drugs. Bacterial gyrase targeted therapeutics are unique strategies to overcome cross-resistance as they are present only in bacteria and absent in higher eukaryotes. The GyrB subunit is essential for the catalytic functions of the bacterial enzyme DNA Gyrase, thereby constituting a promising druggable target. The current study performed a structure-based virtual screening to designing GyrB target-specific candidate molecules. The <i>de novo</i> ligand design of novel hit molecules was performed using a rhodanine scaffold. Through a systematic <i>in silico</i> screening process, the hit molecules were screened for their synthetic accessibility, drug-likeness and pharmacokinetics properties in addition to its target specific interactions. Of the 374 hit molecules obtained through <i>de novo</i> ligand design, qsl-304 emerged as the most promising ligand. The molecular dynamic simulation studies confirmed the stable interaction between the key residues and qsl-304. qsl-304 was synthesized through a one-step chemical synthesis procedure, and the <i>in vitro</i> activity was proven, with an IC₅₀ of 31.23 µg/mL against the novobiocin resistant clinical isolate, <i>Staphylococcus aureus sa</i>-P2003. Further studies on time-kill kinetics showed the bacteriostatic nature with the diminished recurrence of resistance. The on-target gyrB inhibition further proved the efficacy of qsl-304. Communicated by Ramaswamy H. Sarma