Research

Investigate Quorum Signal Synthesis to Manipulate Bacterial Virulence

Research Focus

In the Nagarajan laboratory, we investigate AHL synthase enzymes (I-proteins) to develop quorum sensing inhibitors. Students working in these projects will have the opportunity to learn a variety of tools/skills such as small molecule synthesis, protein expression and purification, protein biochemistry and chemical biology tools, and enzyme kinetics. Depending on the research project, students receive hands-on experience on a broad range of biophysical / analytical instrumentation such as FPLC, HPLC, NMR, Steady State fluorescence, UV-Visible spectrophotometry, colorimetry, stopped flow fluorescence (fast kinetics) etc. We collaborate with structural biologists (X-ray crystallography, biomolecular NMR spectroscopy, Molecular Dynamic simulations etc) to address mechanistic questions in quorum signal synthesis. Students working in these projects also get exposure to bioinformatic tools, molecular visualization tools (Chimera, PyMol etc.) protein homology modeling, and molecular docking tools.

Nicole Cornell

Enzymology

Amrutha Arikkath

Bioinformatics

Jesse Keeler

Protein Biochemistry / Microbiology

                AHL Quorum Sensing. Left: Cartoonish view of QS mechanism. Right: I-protein QS inhibition.

Research Overview

The rapid rise in multidrug resistant organisms pose special challenges to treating bacterial infections. Therefore, therapeutic strategies that combat bacterial virulence without aggravating drug resistance are in great demand. Since antibiotics threaten the survival of microorganism, it puts selective pressure on bacteria to develop resistance. Therefore, compounds that doesn’t directly kill bacteria (antibiotics) but rather limits the microbe’s ability to harm the host (antivirulence) are attractive as novel antimicrobials in antibacterial therapy.

 

When and how does bacteria turn virulent?

A single cell bacterium in the planktonic mode do not have the means to impact the environment. In this state, bacteria are typically avirulent. In most instances however, bacteria seldom remain in the planktonic mode but instead communicate and cooperate with their immediate neighbors to behave like a multicellular species. In the ‘social/group mode’ bacteria makes collective decisions to fight off common threats such as a looming antibiotic attack, immune response from the host during infection, responding to resource strains in the environment etc.  Interbacterial communication helps bacteria transition from an avirulent planktonic state to a virulent social mode. This communication is facilitated by a chemical signal sensing mechanism called “Quorum Sensing”.  


How does Quorum Sensing work?

Bacteria makes specific signal molecules called autoinducers. While Gram-positive bacteria use peptide signaling, Gram-negative bacteria predominantly use Acyl Homoserine Lactones (AHLs) chemical signals to facilitate quorum sensing. A dedicated set of proteins called the I-proteins or AHL synthases make these intracellular AHL signals that are eventually released to the local environment. Since signal strength in the environment reflect local population-levels, bacteria count these signals to estimate its local population density and hence the name quorum sensing (QS). QS informs bacteria if their local population has reached quorum levels necessary to trigger social traits such as forming a biofilm, releasing virulence factors, infecting a host etc. Since a larger population gives bacteria a competitive advantage to survive an immune / antibiotic onslaught, this information is critical for them to judge the optimum timing to infect a host. Quorum sensing inhibitors would interfere with bacteria’s ability to count its population and keep them in an avirulent mode. The long-term focus in our lab is to develop quorum sensing modulators that either inhibit or activate QS in bacteria (can you think of a reason on how QS activators could also become useful tools to fight bacterial infections?). In addition to their biomedical significance, QS modulations may also serve as useful mechanistic probes to study social behavior in bacteria (sociomicrobiology). 

Current Projects

Medicinal Chemistry / Drug Discovery

In this project, we use a medicinal chemistry approach to synthesize a library of AHL QS signal analogs and use them as chemical probes to uncover novel binding pockets in AHL synthases. Student training opportunities in this project include small molecule synthesis, protein purification, enzyme inhibition assays and mechanism of inhibition studies. The outcome of this project will reveal a) new pharmacophores for developing antivirulence-based medicinal compounds and b) mechanistic probes for studying social behavior in bacteria.

Molecular Biophysics

The goal of this project is to develop chemical tools for determining cargo-flipping rates in ACP dependent enzyme. We use a stopped-flow fluorometer to measure pre-steady state kinetics (fast kinetics) in the milliseconds to seconds time range of substrate binding to enzymes. Students working in this project will learn to use genetic code expansion tools to incorporate fluorophores at specific sites in proteins. The tools discovered in this project will reveal the mechanism of carrier protein recognition with their partner enzymes. 

Mechanistic Enzymology

Fidelity / Specificity in signal synthesis is an important aspect of quorum sensing, yet the molecular details on how AHL synthases achieve fidelity in signal synthesis continue to remain poorly resolved. This project involve mechanistic studies on a library of AHL synthases using the tools of protein biochemistry, enzymology, chemoenzymatic synthesis and molecular modeling.

Protein NMR

In this project, we use biomolecular NMR tools (collaboration)  to map protein-protein contact surfaces in AHL signal synthesis. Results from this project will enhance our understanding of substrate recognition in QS signal synthesis and open new doors for developing small-molecules that interrupt protein-protein interface in QS signal synthesis.

Structural Biology

The structural basis of substrate recognition is investigated in this project. We use the tools of X-ray Crystallography (collaboration), protein-ligand docking and MD simulations to discover potent inhibitors for AHL synthases. This project will offer student training opportunities in bioinformatics, docking, homology modelling and molecular dynamics simulations.