R15 AREA: Optimizing allosteric modulation of noncoding regulatory RNA function

Project Summary/AbstractBacterial drug resistance is a significant global health threat that has turned once treatablebacterial infections (including Gram-positive infections) into deadly illnesses. To overcome thisserious threat to human health, completely novel antibiotics are needed. Noncoding ribonucleicacids regulate a wide array of important cellular processes and represent a novel set of targetsfor developing the next generation of therapeutic agents to treat infectious diseases. The T-boxriboswitch is a noncoding RNA that regulates the expression of essential genes in many Gram-positive bacteria (including pathogenic examples), thus making it a unique target for novelantibacterial agents. A key component of the T-box riboswitch regulatory mechanism involvestRNA binding to the highly conserved antiterminator RNA element--an excellent target for drugdiscovery. This project will explore the rational design of allosteric modulators of T-boxantiterminator RNA function and compare their efficacy to that of competitive inhibitors. Notherapeutic agents are currently known to specifically target the T-box riboswitch.This proposal seeks to improve the activity of an initial set of compounds by investigating thehypothesis that leveraging allosteric modulation is an effective drug discovery strategy fortargeting noncoding RNA function. Specific Aims are to 1) Design potent antagonists of T-boxantiterminator function (using computational methods informed by experimental data), 2)Synthesize compounds and screen in 1ｰ assays (assays for antiterminator and riboswitchfunction and preliminary antibacterial screening); and, 3) Characterize compound binding andmechanism of action (quantifying antiterminator binding, riboswitch inhibition and using in vitroand in cellular structure probing methods).Achievement of the proposed specific aims will improve scientific knowledge by developingdesign strategies to identify inhibitors (including allosteric modulators) of RNA function and byexploring the most effective chemical space features of these small molecules. This informationwill be significant for antibacterial drug discovery targeting the T-box riboswitch and also for thestill emerging broader field of targeting noncoding regulatory RNA in general for antibacterial,antiviral, anticancer and other drug discovery efforts. In the process, a team of primarilyundergraduate students will gain first-hand experience working on an innovative drug discoveryproject that will inspire them to consider careers in biomedical research.