“A Game-Changer in Antibiotic Discovery: The Influence of Explainable Deep Learning”

In a significant scientific breakthrough, researchers have unveiled a groundbreaking category of antibiotics, marking the first such discovery in six decades, and more notably, the inaugural achievement through the utilization of AI-driven explainable deep learning. This new class of antibiotics demonstrates remarkable efficacy against multidrug-resistant pathogens, serving as a testament to AI’s transformative potential in the realm of drug discovery and its pivotal role in addressing antibiotic resistance.

This groundbreaking research was conducted collaboratively by a team of 21 experts, including scientists from prestigious institutions such as MIT, the Broad Institute of MIT and Harvard, Integrated Biosciences, the Wyss Institute for Biologically Inspired Engineering, and the Leibniz Institute of Polymer Research in Dresden, Germany. The lead authors of this pioneering study are Dr. Felix Wong, co-founder of Integrated Biosciences, and Dr. James J. Collins, Termeer Professor of Medical Engineering and Science at MIT.

The innovative approach adopted in this study involved the virtual screening of an extensive pool of over 12 million potential compounds to unveil this new class of antibiotics, which exhibits a remarkable capacity to combat antibiotic resistance. What sets this research apart is the implementation of deep learning models trained on experimentally derived data to predict both the antibiotic’s effectiveness and its potential toxicity. Drawing inspiration from AI applications in various domains, including DeepMind’s AlphaGo technology, the researchers devised novel models to elucidate the critical molecular components responsible for antibiotic activity.

The outcome of this research is the identification of a fresh category of antibiotics, demonstrating potent efficacy against multidrug-resistant pathogens. In a series of experiments, a candidate antibiotic was tested in mouse models afflicted with MRSA infection, revealing its efficacy both through topical application and systemic administration. This promising result suggests that this compound holds potential for further development as a treatment for severe bacterial infections, including those associated with sepsis.

Dr. Felix Wong emphasized the groundbreaking nature of this discovery, stating, “This finding underscores the profound impact that artificial intelligence and explainable deep learning can exert on drug discovery. Our research has made accessible a suite of high-precision models capable of accurately predicting both the antibiotic’s efficacy and its potential toxicity. Importantly, it represents one of the initial demonstrations of deep learning models providing clear explanations for their predictions, with profound and far-reaching implications for the future of drug discovery through AI.”

Dr. James J. Collins added, “This breakthrough validates the pivotal role of integrating AI and explainable deep learning in overcoming some of the most formidable challenges in medicine, particularly antibiotic resistance. Leveraging these validating studies and similar approaches, the Integrated Biosciences team is poised to expedite the fusion of synthetic biology and an in-depth understanding of cellular stress, addressing a significant unmet need for novel treatments targeting age-related diseases.”

Satotaka Omori, Ph.D., founding member and Head of Aging Biology at Integrated Biosciences, and a contributing author on the publication, noted, “An important implication of this study is the feasibility and desirability of rendering deep learning models in drug discovery explainable. While AI continues to make substantial inroads, it is also hampered by the opacity of commonly used black box models, which obscure the decision-making process. By unveiling these black boxes, we aim to generate more universally applicable insights, potentially expediting the deployment and development of next-generation approaches to drug discovery.”

Alicia Li, a research associate at Integrated Biosciences and a contributing author to the publication, expressed her enthusiasm, stating, “It is truly exhilarating to witness the establishment of a new methodology for forecasting a compound’s antibiotic utility, its likelihood of progressing through Phase I trials, and its potential membership in a novel class of drugs.”

The research conducted by Integrated Biosciences stands as a testament to the transformative potential of AI, not only in antibiotic discovery but also in the quest for innovative treatments for age-related diseases, as demonstrated in previous publications by the institution. These advancements hold promise in addressing conditions such as fibrosis, inflammation, and cancer.

Reference: “Discovery of a structural class of antibiotics with explainable deep learning,” Nature, 20 December 2023.
DOI: 10.1038/s41586-023-06887-8

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• Nature – Discovery of a structural class of antibiotics with explainable deep learning
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• Integrated Biosciences – Advancements in AI-driven drug discovery