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耐甲氧西林金黄色葡萄球菌（MRSA）和万古霉素中介耐药金黄色葡萄球菌（VRSA）均被世界卫生组织（WHO）列为高优先级致病病原体。在这两类耐药菌中，MRSA是全球报道最为广泛的致病菌，亟需开发新型抗MRSA药物。靶向细菌DNA旋转酶（DNA Gyrase）的治疗策略是克服交叉耐药的独特手段，因为该酶仅存在于细菌中，而高等真核生物体内并无该酶。GyrB亚基是细菌DNA旋转酶催化功能发挥的关键组分，因此是极具潜力的药物作用靶点。本研究采用基于结构的虚拟筛选方法，开发靶向GyrB的特异性候选分子。研究以罗丹宁骨架（rhodanine scaffold）为基础，对新型命中化合物开展从头（de novo）配体设计。通过系统性的虚拟（in silico）筛选流程，本研究在评估候选分子与靶点特异性相互作用的基础上，额外对其合成可及性、成药性及药代动力学特性进行了筛选。在通过从头配体设计获得的374个命中化合物中，qsl-304成为最具开发潜力的配体分子。分子动力学模拟研究证实，qsl-304与靶点关键残基之间可形成稳定的相互作用。研究人员通过一步化学合成法制备了qsl-304，并验证了其体外（in vitro）活性：针对新生霉素耐药的临床分离株金黄色葡萄球菌sa-P2003，其半最大抑制浓度（IC₅₀）为31.23 µg/mL。后续的时间杀菌动力学研究表明，qsl-304具有抑菌活性，且可降低耐药性的复发概率。靶点特异性的gyrB抑制实验进一步证实了qsl-304的药效。本文由Ramaswamy H. Sarma转交。