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January 19, 2021 Webinar Speakers

Welcome to the new year of JAWSChem! Our first webinar of the year 2020 will take place via the internet on Tuesday January 19th at 8pm EST/1am GMT (Jan. 20). Sign up on our mailing list to receive the zoom link!

We look forward to continuing this series well into the future and hop to see/hear from you all at one of our sessions or as one of the next speakers. If you are an early career scientist and would like to present your research don't hesitate to submit an abstract today! For now, please learn more about our current speakers and their research below!

Our featured speakers this week are Dana Stamo (graduate student; University of Colorado Boulder, USA), Erich Hellemann (graduate student; University of Pittsburgh, US), and Professor John Swierk (Assistant Professor; SUNY Binghamton, USA). The seminar will be guest moderated by Professor Kyle F. Biegasiewicz from Arizona State University!



Biography: Dana F. Stamo is a second-year Biological Engineering PhD student at the University of Colorado Boulder where she does research on novel therapeutics for hard-to-treat infectious diseases. In 2019, Dana graduated from the University of Colorado Boulder with her Bachelor’s degree in Chemical & Biological Engineering. An artist in her free time, Dana often blurs the line between art and science, using creativity and design principles in her approach to engineering. When she isn’t doing art or science, you’ll find Dana hiking the Colorado Rockies, skating, or reading.

Title of Talk: Light-Activated Quantum Dot Potentiation of Antibiotics to Treat Drug-Resistant Bacterial Biofilms

Abstract: Antimicrobial resistance is one of the biggest threats to global health and demands alternative therapies for multi-drug resistant (MDR) infections. Light-activated quantum dots (QDs) are a versatile candidate for treating MDR bacteria without harming mammalian cells. Furthermore, their ease of diffusion and ability to photo-potentiate allows for precise, localized treatment and their dynamic tunability keeps them in pace with bacterial evolution. While QDs are shown to be a viable alternative therapy for planktonic cultures, they have not been applied in treating bacterial biofilms (a common growth form that affords bacterial strains more resistance and persistence to immune and traditional drug attack). Additionally, the mechanism of QD attack—production of reactive oxygen species—and sub-breakpoint antibiotic treatments have been shown to stimulate biofilm formation, especially in clinical isolates. Herein, I demonstrate the previously-observed monotherapeutic stimulation of biofilm formation and apply QD-antibiotic combination therapies to overcome and nearly eradicate 48-hour, early-stage, static biofilms. These results lay the groundwork for QD-antibiotic combination treatments for late-stage clinical and industrial biofilms, contributing to the development of QD nanotherapeutics for combating MDR superbugs.

ERICH HELLEMANN (on twitter @ehellemann)

Biography: Erich Hellemann is a Molecular Biophysics and Structural Biology PhD student working at the laboratory of Jacob D. Durrant based at the University of Pittsburgh. He obtained his master’s in chemistry at Carnegie Mellon University with a focus in small molecule NMR. His graduate research focuses on applying and developing computational tools for computer-aided drug discovery (CADD) as well as using molecular simulations to elucidate protein and protein-ligand complexes mechanisms of action.

Title of Talk: Sub-Pocket EXplorer (SubPEx): Leveraging weighted ensemble simulations to enhance the conformational search of binding-pocket conformations

Abstract: Computational methods are extensively used in drug discovery. Virtual screening in particular can ameliorate the costs associated with early-stage hit identification. Standard virtual-screening methods dock flexible compounds into a single, rigid protein receptor. These methods are fast, but they do not take into account all the conformational sub-states that a protein can adopt. Ensemble docking seeks to overcome this limitation by docking candidate ligands into multiple protein conformations. These conformations are often derived from brute-force molecular dynamics (MD) simulations, but standard MD takes too long to thoroughly sample the full conformational landscape. Weighted ensemble (WE) path sampling is an enhanced sampling technique that generates conformational ensembles more efficiently. WE focuses computational efforts on rare-event sampling by encouraging even sampling along a predefined progress coordinate. In this work, we use a novel WE method called SubPEx to obtain ensembles of protein conformations with diverse pocket shapes.

PROF. JOHN SWIERK (on twitter @swierklab)

Biography: John Swierk is an Assistant Professor of Chemistry at Binghamton University (SUNY). He received bachelor degrees in Chemistry and Materials Science & Engineering from the University of Pennsylvania before completing a Ph.D. in Chemistry at the Pennsylvania State University. Prior to joining the faculty at Binghamton he completed postdoctoral appointments at Lawrence Berkeley National Lab as part of the Joint Center for Artificial Photosynthesis and the Yale Energy Sciences Institute, where he was later appointed as an associate research scientist. His research focuses on characterizing radical reactions initiated by single electron transfer, most commonly through photochemical and electrochemical means.

Title of Talk: Mechanistic Investigations of Photoredox Reactions

Abstract: Photoredox catalysis is transforming modern synthetic chemistry. Expensive, hard to handle stoichiometric reagents can be replaced by short-lived excited states using a visible light absorbing photocatalyst. While the scope of photoredox methods has grown at an exceptional pace, mechanistic and kinetic understanding has lagged behind. Using a prototypical alpha-amino arylation reaction as an example, the reaction intermediates and kinetics of each step are determined using a mixture of transient absorption spectroscopy and electrochemical methods. The key rate-limiting step, deprotonation of an amine radical cation, and other unproductive steps are identified. Kinetic modeling is then used to rationalize the design of this reaction and other generalized photoredox reactions. The results from these studies can be used in the design of new photocatalysts and new reaction mechanisms for photoredox catalysis.

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