Lab Members

Yu Chen, Ph.D. – Principal Investigator

Professor, Department of Molecular Medicine, University of South Florida, 2022-Present

Associate Professor, Department of Molecular Medicine, University of South Florida, 2015-2022

Assistant Professor, Department of Molecular Medicine, University of South Florida, 2009-2015

Associate member, Moffitt Cancer Center, 2010-present

Postdoctoral fellow, University of California San Francisco, 2003-2009

Ph.D., Biochemistry and Molecular Biology, University of Chicago, 2002

BS, Biochemistry and Molecular Biology, Peking University, 1997

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Eric Lewandowski, Ph.D. – Research Scientist

Dissertation Title: Structure Based Drug Design Targeting Bacterial Antibiotic Resistance and Alzheimer’s Disease

 

 

 

 

 

 

 

Xiujun “Jun” Zhang, Ph.D. – Research Associate

 

 

 

 

 

 

 

 

Danielle Blazier – 5th Year Ph.D. Student

I graduated from the University of South Florida in 2019 with a BA in Psychology and a BS in Biological Health Sciences. My work focuses on investigating the structural biology of BIN1/Tau interaction and the potential impact molecular chaperones have on BIN1/Tau binding in Alzheimer’s disease.

 

 

 

 

 

 

 

Lian Jacobs – 4th Year Ph.D. Student

I graduated from the University of South Florida in 2019 with my bachelor’s degree in Cell and Molecular Biology. My research focuses on understanding beta-lactamase enzymes, specifically carbapenemases which are capable of hydrolyzing carbapenem antibiotics. Using molecular docking to guide structure-based drug design, we are developing novel inhibitors that are capable of targeting multiple classes of beta-lactamases. I am also investigating the evolution of carbapenemases including their innate ability to hydrolyze carbapenems, with the ultimate goal of disrupting antibiotic resistance in bacterial infection.

 

 

 

 

Patrick Consol – 3rd Year Ph.D. Student

I graduated from Oral Roberts University in 2022 with a bachelor’s degree in biomedical chemistry. My research focus is on the mechanisms of antimicrobial resistance, I hope to determine protein structure via crystallography and use computational methods to develop novel antimicrobial compounds.

 

 

 

 

 

 

 

 

Navita Kohaal – 3rd Year Ph.D. Student

I obtained a Bachelor of Science in Biotechnology from Panjab University, Chandigarh, India, in 2017, and later completed a Master’s degree in Biotechnology from the same institution in 2019. My research interests are centered around deepening my understanding of crystal structures and investigating the effectiveness of inhibitors in preventing human diseases. Specifically, my current research is focused on crystallizing Mpro, which is the main protease of SARS-CoV-2, and evaluating its behavior when exposed to multiple inhibitors.

 

 

 

 

 

 

 

Clem Marsilia – 2nd Year Ph.D. Student

I graduated from the University of South Florida in 2023 with a B.S. in Biomedical Sciences. My research is focused on gaining insights into the lytic and endodyogeny cycles of Toxoplasma gondii. Specifically, I am focused on studying how these fundamental processes are influenced by TgCrk2 and its various cyclin partners.

 

 

 

 

 

 

 

Ya-Tzu Li – 1st Year Ph.D. Student

I graduated from Tzu Chi University in Taiwan with a background in life sciences and am currently a pharmaceutical nanotechnology master’s student conducting virtual drug screening for the GPCR targets b2ar and TAS2R14, aiming to develop novel therapeutic strategies for the treatment of various diseases using docking and AWS for large-scale drug screening. I am extremely passionate about exploring new technologies and methods to optimize drug discovery and design, especially in the GPCRs.

I am a third-year undergraduate student who will be graduating with a B.S. in Biology with a concentration in medical biology in July 2024. Currently, my research is focused on crystallizing a number of different protein types such as GpsB, MraZ, and FKBP51.

 

 

 

 

 

 

 

Alumni – Ph.D. Students

Shane Butler, Ph.D. – 2022

I obtained my bachelor’s degree in Biochemistry from Queen’s University, Kingston, Canada, in 2019, and my master’s degree in Biochemistry from Western University, London, Canada, in 2021. My work will focus on the structural and functional characterization of cell wall transpeptidases in C. difficile physiology and virulence. Understanding how these enzymes contribute to the fitness of C. difficile, including antibiotic resistance, will provide a basis for structure-based drug design of inhibitors against C. difficile sporulation and growth.

 

 

 

 

 

 

 

 

Michael T. Kemp, Ph.D. – 2021

Dissertation Title: Mechanistic Insight into Beta-Lactamase Catalysis, Inhibitor Design, and Resistance

 

 

 

 

 

 

 

Michael Sacco, Ph.D. – 2021

Dissertation Title: Targeting Modern Pathogens with Rational Drug Design

 

 

 

 

 

 

 

Afroza Akhtar, Ph.D. – 2020

Dissertation Title: Structure Based Inhibitor Discovery Targeting Multiple Beta-lactamases Involved in Antibiotic Resistance

 

 

 

 

 

Kyle Kroeck, Ph.D. – 2019

Dissertation Title: Targeting Bacterial Resistance and Cancer Metastasis: A Structure Based Approach

 

 

 

 

 

 

Orville Pemberton, Ph.D. – 2017

Dissertation Title: Mechanism Elucidation and Inhibitor Discovery against Serine and Metallo-Beta-Lactamases Involved in Bacterial Antibiotic Resistance

 

 

 

 

 

 

Emmanuel Smith, Ph.D. – 2014

Dissertation Title: Computer-Aided Structure-Based Drug Discovery: CXCL12, P. aeruginosa LpxA, and the Tiam1 PDZ Domain

 

 

 

 

 

Derek Nichols, Ph.D. – 2014

Dissertation Title: Structure-Based Design of Novel Inhibitors and Ultra High Resolution Analysis of CTX-M Beta-Lactamase

 

 

 

 

Alumni – Masters/Undergraduate Students

Aiden Jaskolka-Brown – Undergraduate Volunteer

 

 

 

 

 

 

 

Krishna Narramneni – Undergraduate Volunteer

I graduated from The University of Tampa in 2022 with my bachelor’s degree in biology with a molecular concentration and a minor in chemistry. I am currently working on my master’s degree in bioinformatics and computational biology at USF. In the Chen Lab, I am currently working on molecular docking with USP11 and how it’s potentially involved in neurodegenerative diseases. I am also interested in learning more about RNA biology and its potential in molecular docking and as a new drug target.

 

 

 

 

 

 

 

Anna Jablonska – Undergraduate Volunteer

My current research is focused on crystallizing MPro and PLPro, which are the main SARS-CoV-2 proteases, with multiple inhibitors. I hope to further my research by working on inhibition assays for β-lactamases and PLPro.

 

 

 

 

 

 

 

 

Maura Gongora – Masters Student/Research Assistant

I am expanding my repertoire of molecular biology techniques in the Chen lab to further a career in the Biotechnology field. My work involves the crystallization of Mpro, the main protease of SARS-CoV-2, with multiple inhibitors.

 

 

 

 

Ryan Morgan

My work in the lab focused on crystallization and inhibition assays on two protein systems: β-lactamases and the main protease from SARS-CoV-2 (M^pro). I identified fragment compounds that were effective against both serine and metallo β-lactamases which can be linked together to design a broad-spectrum inhibitor. Combined with structural data, a broad-spectrum inhibitor could provide insight on how to target β-lactamases to mitigate antibiotic resistance. My work on crystallization of M^pro from SARS-CoV-2 helped obtain apo and complex structures of previously unseen mutants. This data aids in our understanding of how drugs targeting M^pro_, such as Pfizer’s Paxlovid, could become less effective due to changes in the active site structure.

 

 

Nick Torelli

In my specific research project, I have focused on a fragment-based approach to develop novel inhibitors against class A beta-lactamases such as TEM-1, TEM-24, SHV-2 and CTX-M. I utilize virtual screening to identify novel, non-covalent inhibitors against TEM, SHV-2, and CTX-M. I have identified inhibitors against multiple beta-lactamases and solved the complex structures using X-ray crystallography, the lead optimization process. In addition to this work, I have presented six different presentations, one of which was at the 248th ACS National Meeting in San Francisco, CA.

 

 

 

 

 

Cody Johnson

Using X-ray crystallography and computational molecular docking in a fragment-based approach, I am searching for novel inhibitors for the bacterial proteins Mtg and SecA with the hope of developing new treatments for these enticing drug targets. Mtg aids in peptidoglycan maintenance while SecA is part of a pathway that secretes other proteins into the cell’s periplasm. Both proteins serve essential roles that aid in cell survival and need to be studied more closely to find compounds that can inhibit their function.