Abstract
Antibiotic resistance and pathogenic infections underscore the importance and urgency of novel control agent development. Bio-based products represent a rich reservoir of antimicrobial agents. However, traditional strategies for screening new active compounds are time-consuming, costly, and limited by accessible resources. Here, transcriptomic combinatorial molecular docking (TCMD), a novel method enabling fast identification of antimicrobial components in complex mixtures without requiring prior knowledge is proposed. Results show that, in eukaryotic microorganism systems, TCMD demonstrates superior performances in screening antifungal compounds within hydrothermal liquefaction aqueous. The high accuracy is confirmed by molecular dynamics simulation, antifungal experiments, and RT-qPCR (reverse transcription real-time quantitative polymerase chain reaction) analysis. Furthermore, TCMD exhibits cross-system applicability, as evidenced by successful antibacterial substances screening in prokaryotic systems using plant essential oil and traditional Chinese medicine from previous studies. Compared to conventional approaches, TCMD is estimated to be 3-20 times faster and ≈10 times more cost-effective, while maintaining high-throughput capacity for analyzing thousands of compounds simultaneously. These demonstrate that TCMD is a rapid, precise, and flexible method for antimicrobial compound discovery, significantly accelerating the development of new antibacterial agents.