Artificial Intelligence (AI) for Antibiotic Discovery
Wednesday, November 6, 2024
2:30 PM-4:00 PM
BIOMED Seminar
Title:
Artificial Intelligence (AI) for Antibiotic Discovery
Speaker:
César de la Fuente Nunez, PhD
Presidential Assistant Professor
Machine Biology Group
Institute for Biomedical Informatics
Institute for Translational Medicine and Therapeutics
Penn Institute for Computational Science
University of Pennsylvania
Details:
Computers excel at superhuman pattern recognition in images and text; however, their application in biology and medicine is still in its infancy. In this talk, I will discuss our advances over the past decade, which are accelerating discoveries in the crucial and underinvested area of antibiotic discovery. We have pioneered the design of antibiotics using artificial intelligence (AI), achieving proven efficacy in preclinical animal models and demonstrating that machines can effectively create therapeutic molecules. For the first time, we successfully mined the human proteome to identify antibiotic candidates. Building on this success, we hypothesized that similar compounds could be found throughout evolution. We expanded our efforts to extinct species, where our AI-driven approach led to the discovery of the first therapeutic molecules from organisms such as Neanderthals and the woolly mammoth. This work launched the field of molecular de-extinction and yielded preclinical candidates such as neanderthalin, mammuthusin, and elephasin. Furthermore, my lab has broadened our antibiotic discovery initiatives to explore other branches of the tree of life beyond eukaryotes.
By computationally analyzing microbial dark matter, we identified nearly one million new antibiotic molecules. These molecules have been made freely available and open access to the scientific community to encourage researchers worldwide to synthesize, characterize, and further develop them. This collaborative effort leveraged machine learning to explore the vast diversity of the microbial world by analyzing 63,410 metagenomes and 87,920 microbial genomes. Additionally, through the computational exploration of thousands of human microbiomes, we and our collaborators discovered a myriad of new antimicrobial agents, including prevotellin-2 produced by the gut microbe Prevotella copri. Collectively, our efforts have dramatically accelerated antibiotic discovery, reducing the time required to identify preclinical candidates from years to just a few hours. I believe we are on the cusp of a new era in science where advances enabled by AI will help control antibiotic resistance, infectious disease outbreaks, and pandemics.
Biosketch:
César de la Fuente Nunez, PhD, is a Presidential Assistant Professor at the University of Pennsylvania, where he leads the Machine Biology Group, whose goal is to combine the power of machines and biology to help prevent, detect and treat infectious diseases. Specifically, he pioneered the development of the first antibiotic designed by a computer with efficacy in animals; designed algorithms for antibiotic discovery; reprogrammed venoms into antimicrobials; created novel resistance-proof antimicrobial materials and invented rapid low-cost diagnostics for COVID-19 and other infections.
Prof. de la Fuente Nunez is an NIH MIRA investigator and has received recognition and research funding from numerous other groups. He has received over 50 awards. He was recognized by MIT Technology Review as one of the world’s top innovators for “digitizing evolution to make better antibiotics.” He was selected as the inaugural recipient of the Langer Prize, an ACS Kavli Emerging Leader in Chemistry, and received the AIChE’s 35 Under 35 Award and the ACS Infectious Diseases Young Investigator Award. In 2021, he received the Thermo Fisher Award and the EMBS Academic Early Career Achievement Award for “the pioneering development of novel antibiotics designed using principles from computation, engineering and biology.” Most recently, Prof. de la Fuente Nunez was awarded the prestigious Princess of Girona Prize for Scientific Research, the ASM Award for Early Career Applied and Biotechnological Research, and was named a Highly Cited Researcher by Clarivate.
Prof. de la Fuente Nunez has given over 150 invited lectures and his scientific discoveries have yielded multiple patents and ~100 publications, including papers in Nature Biomedical Engineering, Nature Communications, PNAS, ACS Nano, Cell, Nature Chemical Biology, and Advanced Materials.
Contact Information
Carolyn Riley
cr63@drexel.edu