Discovery of Novel Antimicrobial-Active Compounds and Their Analogues by In Silico Small Chemical Screening Targeting Staphylococcus aureus MurB

Methicillin-resistant <i>Staphylococcus aureus</i> is a serious problem in healthcare due to its lethal severe infections and resistance to most antimicrobial agents. The number of new approved antimicrobial agents is declining, and combined with the spread of drug-resistant bacteria, it is predicted that effective antimicrobial agents against multidrug-resistant bacteria will be exhausted. We conducted in silico and in vitro discovery of novel antimicrobial small molecules targeting the SaMurB enzyme involved in cell wall synthesis in <i>Staphylococcus aureus</i> (<i>S. aureus</i>). We performed hierarchical structure-based drug screenings to identify compounds and their analogues using a library of approximately 1.3 million compound structures. In vitro experiments with <i>Staphylococcus epidermidis</i> (<i>S. epidermidis</i>) identified three compounds (SH5, SHa6, and SHa13) that exhibit antibacterial activity. These three compounds do not have toxicity against human-derived cells. SHa13 exhibited remarkable activity (IC₅₀ value =1.64 ± 0.01 µM). The active compound was predicted to bind to the active site of SaMurB by forming a hydrogen bond with Arg188 in both R and S bodies. These data provide a starting point for the development of novel cell wall synthesis inhibitors as antimicrobial agents targeting SaMurB.