Clear Research Group

Work in the Clear lab integrates themes from organic, physical, and analytical chemistry to address questions regarding recognition of biologically important anions.is in the area of bioorganic and supramolecular chemistry, with general interests in the following areas:

Importantly, students participating in research will be exposed to a range of techniques, from traditional organic synthesis to binding studies requiring repetitive measurement and extensive data analysis. As a result, this research experience will help train students for graduate and professional studies as well as careers in industry.

A. Polymeric Materials for Phosphate Removal from Water
Phosphate is an essential nutrient for health in all living organisms. However, elevated levels of phosphate and phosphate derivatives can have destructive effects on human health and on the environment. There is a need for agents that can remediate these issues by sequestering the phosphate species from water through adsorption to an insoluble nanostructure and removing the anions from the solution, as illustrated below. This need is evidenced in part by the large number of recent studies being published on the topic, and there is particular interest in developing effective and efficient strategies for removing phosphate from both environmental water and wastewater. We are currently synthesizing new polymeric networks and studying their capacity for binding phosphate and to learn about the structural determinants of binding capacity, phosphate selectivity, and degree of swelling. The reference point for the studies will be the polyammonium structure found in sevelamer hydrochloride, and the effect of replacing some or most of the ammonium (charged amino) groups in the polymer with guanidinium (charged guanidino) groups will be examined.
Techniques/Instrumentation: organic synthesis, materials characterization, UV/Vis absorbance spectroscopy, binding analysis
Additional Reading:

• Hydrogels for anion removal from water, J. Mater. Chem. A, 2019, 7, 1394 (Review)
• Phosphate pollution: A global overview of the problem, from Phosphorus: Polluter and resource of the future, 2018, IWA Publishing (Book Chapter)
• Kinetic and thermodynamic evaluation of phosphate ions binding onto sevelamer hydrochloride, I. J. Pharm, 2014, 474, 25

B. Sensor for Anionic Signaling Lipids
The main objective of this work is to generate low molecular weight sensors with the ability to cross cell membranes, bind to phosphatidylinositol phosphate lipids (PIPn) in the membrane, and report the binding event through a fluorescent response. The PIPn lipids are a family of biomolecules that play crucial roles in communication within and between living cells. PIPn lipids are usually found on the interior membranes in animal cells, and their localization within cells and dynamic changes in their distribution are the basis for many cell signaling events. It is also known that dysregulation of PIPn levels is a feature of many diseases. Sensors with the ability to recognize and bind PIPn have the potential to be powerful research tools for understanding key signaling pathways, protein-ligand interactions, and protein-lipid interactions. Thus far, most PIPn sensors have been fluorescently labeled protein or antibody receptors that image localization and dynamics of the lipids. A significant issue with protein-based PIPn sensors is that they have to be introduced by either genetic expression or microinjection for use in cellular studies since proteins cannot diffuse across the cell membrane and the lipids are typically present within cells and interior membranes. We are studying sensors that consist of a membrane permeable synthetic receptor (SR) designed to selectively recognize and bind to the inositol phosphate (IPn) headgroup on the lipid linked to a fluorescent dye that changes signals when it is brought to the membrane surface through the lipid-receptor interaction. Our underlying structural hypothesis of this proposal is that synthetic receptors with combinations of phosphate recognition units and boronic acids, will retain unique affinity for different PIPn while retaining the ability to cross cell membranes.
Techniques/Instrumentation: organic synthesis, chromatography, NMR spectroscopy, fluorescence spectroscopy, liposome preparation, binding analysis
Further reading:

• Synthetic Receptors for Polar Lipids, from Synthetic Receptors for Biomolecules, 2015, RSC Publishing (Book Chapter)
• Cell Permeable Ratiometric Fluorescent Sensors for Imaging Phosphoinositides, ACS Chem. Biol., 2016, 11, 1834
  

C. Recognition and Sensing of Urushiol
Allergic contact dermatitis (ACD) is caused by exposure to urushiol, an oily sap derived from poison ivy/oak/sumac, and it affects approximately 50 million people annually. Urushiol is composed of a catechol functional group bound to a hydrocarbon chain with varying length and degrees of unsaturation. The sensitivity to urushiol is cause by the absorption of this sap through the skin where it binds to proteins and elicits an allergic response leading to a rash and itching. Although prevention of exposure to urushiol is recommended, it is difficult to prevent exposure since urushiol can be transferred by contaminated surfaces such as animal fur, clothing or outdoor tools and those exposed may not be aware until their body has already begun to mount a allergic response. In the lab, we are synthesizing urushiol and studying its encapsulation by cyclodextrin, a cone-shaped oligosaccharide. We are also investigating the effect of boronic acid functionalization of the cyclodextrin to increase the affinity and selectivity for urushiol over other lipid-like molecules. Eventually, the group would like to create a sensor to detect urushiol on surfaces.
Techniques/Instrumentation: organic synthesis, chromatography, NMR spectroscopy, fluorescence spectroscopy, binding analysis
Further reading:

• Synthetic Receptors for Polar Lipids, from Synthetic Receptors for Biomolecules, 2015, RSC Publishing (Book Chapter)
• Biobased Polymer Coating Using Catechol Derivative Urushiol, Langmuir, 2016, 32, 4619

Graduate Publications:
7. Harmatys, K. M., Musso, A. J., Clear, K. J., Smith, B. D. (2016) Small molecule additive enhances cell uptake of 5-aminolevulinic acid and conversion to protoporphyrin IX. Photochem. Photobiol. Sci. Advance Article, DOI: 10.1039/C6PP00151C Link
6. Rice, D. R., Clear, K. J., Smith, B. D. (2016) Imaging and therapeutic applications of zinc(ii)-dipicolylamine molecular probes for anionic biomembranes. Chem. Commun. 52, 8787-8801 Link
5. Clear, K. J., Virga, K., Gray, L., and Smith, B. D. (2016) Using membrane composition to fine-tune the pKa of an optical liposome pH sensor. J. Mater. Chem. C 4, 2925-2930 Link
4. Clear, K. J., Harmatys, K. M., Rice, D. R., Wolter, W. R., Suckow, M. A., Wang, Y., Rusckowski, M., and Smith, B. D. (2016) Phenoxide-bridged zinc(II)-bis(dipicolylamine) probes for molecular imaging of cell death. Bioconjugate Chem. 27, 363-375 Link
3. Clear, K. J. and Smith, B. D. (2015) Synthetic Receptors for Polar Lipids. Synthetic Receptors for Biomolecules, Monographs in Supramolecular Chemistry, Royal Society of Chemistry: pp 405-436 Link
2. Plaunt, A. J., Clear, K. J., and Smith, B. D. (2014) 19F NMR indicator displacement assay using a synthetic receptor with appended paramagnetic relaxation agent. Chem. Commun. 50, 10499-10501 Link
1. Clear, K. J., Stroud, S., and Smith, B. D. (2013) Dual colorimetric and luminescent assay for dipicolinate, a biomarker of bacterial spores. Analyst 138, 7079-7082 Link