A machine learning method for predicting molecular antimicrobial activity

In response to the increasing concern over antibiotic resistance and the limitations of traditional methods in antibiotic discovery, we introduce a machine learning-based method named MFAGCN. This method predicts the antimicrobial efficacy of molecules by integrating three types of molecular fingerprints-MACCS, PubChem, and ECFP-along with molecular graph representations as input features, with a specific focus on molecular functional groups. MFAGCN incorporates an attention mechanism to assign different weights to the importance of information from different neighboring nodes. Comparative experiments with baseline models on two public datasets demonstrate MFAGCN's superior performance. Additionally, we conducted an analysis of the functional group distribution in both the training and test sets to validate the model's predictions. Furthermore, structural similarity analyses with known antibiotics are performed to prevent the rediscovery of established antibiotics. This approach enables researchers to rapidly screen molecules with potent antimicrobial properties and facilitates the identification of functional groups that influence antimicrobial performance, providing valuable insights for further antibiotic development.