Rapid High-Throughput Discovery of Molecules With Antimicrobial Activity From Natural Products Enabled by a Nanoliter Matrix SlipChip

Abstract

Improper use of antibiotics has led to the development of antimicrobial resistance, or “superbugs,” outpacing the discovery of new antibiotics. The lack of rapid, high-throughput screening methods is a major bottleneck in discovery novel antibiotics. Traditional methods consume significant amounts of samples, making it challenging to discover new antibiotics from limited natural product extracts. Here, a rapid, high-throughput screening method is reported for natural products with antimicrobial activity enabled by a nanoliter matrix SlipChip (nm-SlipChip). This nm-SlipChip creates a screening matrix with nanoliter droplets for 100 drug candidate–bacterium combinations. The effectiveness of candidate antibiotics is assessed by analyzing microbial phenotypic changes. This nm-SlipChip reduces sample consumption by over 5000-fold and shortens the detection time to three hours. Twenty compounds isolated from Callicarpa integerrima were tested against 10 pathogenic bacteria and identified two previously unreported clerodane diterpenes with activity against methicillin-resistant Staphylococcus aureus (MRSA). Molecular docking and fluorescence probe experiments reveals that their antimicrobial effect results from disruption of bacterial cell membranes and biofilms. The nm-SlipChip provides an effective method for discovering new antimicrobial drugs from natural sources, vital in combating antibiotic resistance.