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TCMD: A High-Throughput and Rapid Method for Screening Antimicrobial Ingredients from Renewable Bio-Based Resources
Yongdong Xu1,2, Yueyao Wang1, Yongming Chen3
1Laboratory of Environment-Enhancing Energy (E2E), Key Laboratory of Agricultural Engineering in Structure and Environment of Ministry of Agriculture and Rural Affairs, College of Water Resources and Civil Engineering, China Agricultural University, Beijing, 100083, China.
A new method, transcriptomic combinatorial molecular docking (TCMD), rapidly identifies antimicrobial compounds in complex mixtures. This approach accelerates the discovery of novel antifungal and antibacterial agents, overcoming limitations of traditional screening methods.
Area of Science:
- Biotechnology and Cheminformatics
- Antimicrobial Discovery
Background:
- Antibiotic resistance and pathogenic infections necessitate urgent development of new control agents.
- Bio-based products offer a vast source of antimicrobial compounds, but traditional screening is inefficient.
- Existing methods for identifying antimicrobial agents are time-consuming, expensive, and resource-limited.
Purpose of the Study:
- To introduce transcriptomic combinatorial molecular docking (TCMD) as a novel, rapid method for identifying antimicrobial components.
- To demonstrate TCMD's effectiveness in complex mixtures without prior knowledge of compounds.
- To validate TCMD's accuracy and applicability across different biological systems.
Main Methods:
- Transcriptomic combinatorial molecular docking (TCMD) was developed for high-throughput screening.
- TCMD was applied to identify antifungal compounds in hydrothermal liquefaction aqueous (eukaryotic system).
- Method validation included molecular dynamics simulation, antifungal experiments, and RT-qPCR analysis.
- Cross-system applicability was tested by screening antibacterial agents in prokaryotic systems.
Main Results:
- TCMD demonstrated superior performance in screening antifungal compounds from hydrothermal liquefaction aqueous.
- High accuracy of TCMD was confirmed through molecular dynamics, antifungal assays, and RT-qPCR.
- TCMD successfully identified antibacterial substances in prokaryotic systems, showcasing cross-system applicability.
- TCMD is 3-20 times faster and ≈10 times more cost-effective than conventional methods.
Conclusions:
- TCMD is a rapid, precise, and flexible method for discovering antimicrobial compounds.
- The method significantly accelerates the development of novel antibacterial and antifungal agents.
- TCMD overcomes the limitations of traditional screening, offering a high-throughput solution.
