University of Oklahoma

HELEN I. ZGURSKAYA

Mechanistic biochemistry and microbiology, antibiotic resistance

Dr. Zgurskaya research is focused on understanding of molecular mechanisms of multidrug efflux in the context of two membranes and synergistic relationship between efflux transporters and the outer membrane barrier in Gram-negative bacteria. Studies by the HZ group led to the development of currently accepted models of drug efflux across the outer membrane of Gram-negative bacteria.

VALENTIN V. RYBENKOV

Mechanistic biochemistry, cell biology and molecular biophysics

The hallmark of Dr. Rybenkov research is the synergistic use of computer modeling and diverse experimental techniques, which range from single molecule biophysics to cell biology and genetics. Using this approach, Rybenkov and coworkers have deduced complex biochemical mechanisms including topology simplification by DNA topoisomerases, chromosome organization by condensins and kinetics of drug uptake by bacteria.

ADAM DUERFELDT

Organic and medicinal chemistry

The Duerfeldt laboratory integrates synthetic/medicinal chemistry, chemical and structural biology, and computational methods to develop chemical probes and therapeutic leads for unexploited targets implicated in bacterial pathogenesis. His approach aims to identify both natural product and small molecule modulators that cause detrimental effects to bacteria through pathway or enzyme activation, rather than inhibition.

Saint Louis University School of Medicine

JOHN K. WALKER

Organic and medicinal chemistry

Dr. Walker has extensive experience and background in drug discovery and development.  Prior to coming to academia he spent 12 years in the Pharmaceutical industry. He worked on a number of translational projects aimed at bringing new medicines to the clinic that targeted protein kinases such as p38, Janus kinase and Zap-70. More recently, in his academic career, he has collaborated with Zgurskaya and Rybenkov to develop molecules to inhibit the AcrAB-TolC efflux pump of E. coli targeting for the first time the membrane fusion protein AcrA.

Memorial Sloan Kettering Cancer Center

DEREK S. TAN

Organic and medicinal chemistry

Dr. Tan research focuses on the discovery and development of new chemical probes to address a variety of novel antibiotic targets, using both rational drug design and diversity-oriented synthesis. The Tan group has extensive experience in organic synthesis, medicinal chemistry, cheminformatics, pharmacology, and chemical biology to support these efforts, as well as a strong history of successful multidisciplinary collaborations with biologists, and has advanced multiple chemotypes through preclinical pharmacology to in vivo proof-of-concept in animal models.

University of Cagliari, Italy

PAOLO RUGGERONE

Theoretical and computational biophysics

Dr. Ruggerone’s group has addressed several questions related to bacterial physiology and to antibiotic resistance mechanisms. He designed a research project leading to the first article reporting the results of a computational work on an RND transporter (AcrB). Several techniques to study efflux systems at different levels of accuracy are available in his group and used at different stages of the project.

ATTILIO VARGIU

Theoretical and computational biophysics

Dr. Vargiu’s activity in the field of bacterial resistance is strongly focused on the understanding of efflux mechanisms and routes of inhibition of RND efflux pumps. He contributed to the setup and development of several computational protocols for studies of efflux systems at various levels of accuracy.

GIULIANO MALLOCI

Computational modeling and database management

In the research area of antibacterial resistance, in particular, Dr. Malloci recently performed extensive quantum mechanical, classical and docking simulations and collected all data in freely available databases: the database of static and dynamical properties of antimicrobial compounds and the results of a systematic blind docking campaign of different antibiotics targeting AcrB.

Oak Ridge National Laboratory

JEREMY SMITH

Theoretical and computational biophysics

Dr. Smith has performed and directed research in high-performance computer simulation of biological macromolecules, neutron scattering in biology, the physics of proteins, enzyme catalysis, bioenergy, environmental biogeochemistry and the analysis of structural change in proteins. As of 2017 he had published over 400 peer-reviewed scientific articles.

JERRY M. PARKS

Computational chemistry

Dr. Parks’ background is in computational chemistry, biophysics, and structural bioinformatics, with an emphasis on investigating the structure, function and mechanism of bacterial proteins and enzymes. In collaboration with Helen Zgurskaya from the University of Oklahoma, he is developing inhibitors of the AcrAB-TolC multidrug efflux pump from E. coli and using machine learning to identify “rules” of antibiotic permeation in E. coli and P. aeruginosa.

Georgia Institute of Technology

JC GUMBART

Theoretical and Computational Physics

Dr. Gumbart is an expert in computational simulations of complex biophysical phenomena involving proteins and other biomolecules. Recently, an allocation of 38 million processor hours from DOE’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program supported Gumbart lab’s efforts to simulate the shape and related stability of AcrA as it interacts with other efflux pump components.

Los Alamos National Laboratory

S. GNANAKARAN

Theoretical and computational biophysics

Dr. Gnanakaran has led a multi-million dollar LANL/DOE project on the multiscale modeling of efflux pump mediated antibiotic resistance where they developed a framework to understand how structural, genetic, and cellular processes contribute to bacterial antibiotic resistance of Pseudomonas aeruginosa and Burkholderia pseudomallei. The team combined experiment and theory to understand each process, tested and validated computational models, and identified key parts of each process that can be manipulated, paving the way for future work to combat drug resistance.

CESAR LOPEZ

Theoretical and computational biophysics

Dr. Lopez is passionate about unraveling the complex interplay between different macromolecules and cell lipid membranes. During his training and research stages, he has been involved in studying membranes at three different levels: from very simple lipid models, to more sophisticated systems such as the plasma cell membrane.