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MEAM Seminar: “AI for Antibiotic Discovery”
February 13 at 10:00 AM - 11:30 AM
Computers can be programmed for superhuman pattern recognition of 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 half-decade, which are accelerating discoveries in the crucial and underinvested area of antibiotic discovery. We developed the first antibiotic designed by a computer with proven efficacy in preclinical animal models, demonstrating that machines and artificial intelligence (AI) could be used to design therapeutic molecules. Our algorithms have accelerated antibiotic discovery, and for the first time, we successfully mined the human proteome for antibiotics. Recently, we expanded our proteome-mining efforts to explore the proteomes of extinct species. Using AI, my lab discovered the first therapeutic molecules in extinct organisms, including Neanderthals and Denisovans, launching the field of molecular de-extinction. Collectively, our efforts have dramatically reduced the time needed to discover preclinical antibiotic candidates from years to 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.
César de la Fuente
Presidential Assistant Professor, University of Pennsyvania
César de la Fuente is a Presidential Assistant Professor at the University of Pennsylvania, where he leads the Machine Biology Group. Previously, he pursued postdoctoral research at the Massachusetts Institute of Technology (MIT) and earned a PhD at the University of British Columbia (UBC). His research goal is to use the power of machines to accelerate discoveries in biology and medicine. Specifically, he pioneered the development of the first computer-designed antibiotic with efficacy in animal models, demonstrating the application of AI for antibiotic discovery and helping launch this emerging field. His lab has also been in the vanguard of developing computational methods for proteome mining, leading to the breakthrough discovery of a whole new world of antimicrobials. These efforts explored the human proteome as a source of antibiotics for the first time and have dramatically accelerated the time needed to discover preclinical candidates, from years to hours. De la Fuente’s group was also the first to find therapeutic molecules in extinct organisms, launching the field of molecular de-extinction. Additional advances from his lab include designing algorithms for antibiotic discovery, reprogramming venoms into antimicrobials, creating novel resistance-proof antimicrobial materials, and inventing rapid, low-cost diagnostic devices for COVID-19 and other infections. Prof. de la Fuente is an NIH MIRA investigator and has received recognition and research funding from numerous other groups. De la Fuente has received over 65 national and international awards. He is an elected Fellow of the American Institute for Medical and Biological Engineering (AIMBE), becoming one of the youngest ever to be inducted. 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 and as an ACS Kavli Emerging Leader in Chemistry, an ASM Distinguished Lecturer, Waksman Foundation Lecturer, and received the AIChE’s 35 Under 35 Award, Society of Hispanic Professional Engineers Young Investigator Award, and the ACS Infectious Diseases Young Investigator Award. He also received the Thermo Fisher Award, as well as 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 was awarded the prestigious Princess of Girona Prize for Scientific Research, the ASM Award for Early Career Applied and Biotechnological Research, the Rao Makineni Lectureship Award by the American Peptide Society, and was selected as a National Academy of Medicine Emerging Leader in Health and Medicine. De la Fuente serves on the editorial boards of more than 20 scholarly journals and is currently an Associate Editor of Drug Resistance Updates (IF= 24.3; the premier international drug resistance journal), Nature Communications Biology, Bioengineering & Translational Medicine, Bioactive Materials, and Digital Discovery. He has been named a Highly Cited Researcher by Clarivate several times. Prof. de la Fuente has given over 230 invited lectures, including numerous Keynote and Named Lectures, and has spoken at TEDx. He has co-authored a book on machine learning for drug discovery and his scientific discoveries have yielded multiple patents and over 130 publications, including papers in Science, Cell Host Microbe, Nature Biomedical Engineering, Nature Communications, PNAS, ACS Nano, Cell, Nature Chemical Biology, and Advanced Materials.