Fragment-Based Ligand Discovery Using Protein-Observed 19F NMR: A Second Semester Organic Chemistry CURE Project

Curriculum-based undergraduate research experiences (CUREs) have been shown to increase student retention in STEM fields and are starting to become more widely adopted in chemistry curricula. Here we describe a 10-week CURE that is suitable for a second-semester organic chemistry laboratory course. Students synthesize small molecules and use protein-observed ¹⁹F (PrOF) NMR to assess the small molecule's binding affinity to a target protein. The research project introduced students to multistep organic synthesis, structure-activity relationship studies, quantitative biophysical measurements (measuring K_d from PrOF NMR experiments), and scientific literacy. Docking experiments could be added to help students understand how changes in a ligand structure may affect binding to a protein. Assessment using the CURE survey indicates self-perceived skill gains from the course that exceed gains measured in a traditional and an inquiry-based laboratory experience. Given the speed of the binding experiment and the alignment of the synthetic methods with a second-semester organic chemistry laboratory course, a PrOF NMR fragment-based ligand discovery lab can be readily implemented in the undergraduate chemistry curriculum.

Chitin structure and chitinase activity: isolation of structurally intact chitins

Assessment of chitinase kinetics and mechanism in vitro has been hampered by lack of suitable substrates. We have previously reported rapid linear initial chitinase velocity with chitin substrate isolated from insect larval cuticle. Such chitin is shown to be fibrous in the light microscope. Methods are described for preparing fibrous chitins from any animal source including calcified carapaces. Evidence is given that chitin native fine structure in situ is maintained by structural proteins which in the fibrous chitin isolates are functionally replaced by covalently bound ester groups. Chitin fiber analogues thus reconstructed appear to have retained their native fine structure.