Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Bur SK

PROVIDER: S-EPMC10237086 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Publications

Fragment-Based Ligand Discovery Using Protein-Observed <sup>19</sup>F NMR: A Second Semester Organic Chemistry CURE Project.

Bur Scott K SK Pomerantz William C K WCK Bade Morgan L ML Gee Clifford T CT

Journal of chemical education 20210511 6

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 <sup>19</sup>F (PrOF) NMR to assess the small molecule's binding affinity to a target protein. The research project introduced students to ...[more]

PMID: 37274366

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Project description:Inhibitor discovery for protein-protein interactions has proven difficult due to the large protein surface areas and dynamic interfaces involved. This is particularly the case when targeting transcription-factor-protein interactions. To address this challenge, structural biology approaches for ligand discovery using X-ray crystallography, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy have had a significant impact on advancing small molecule inhibitors into the clinic, including the U.S. Food and Drug Administration approved drug, Venetoclax. Inspired by the protein-observed NMR approach using 1H-15N-HSQC NMR which detects chemical shift perturbations of 15N-labeled amides, we have applied a complementary protein-observed 19F NMR approach using 19F-labeled side-chains that are enriched at protein-protein-interaction interfaces. This protein-observed 19F NMR assay is abbreviated PrOF NMR to distinguish the experiment from the more commonly employed ligand-observed 19F NMR methods. In this Account, we describe our efforts using PrOF NMR as a ligand discovery tool, particularly for fragment-based ligand discovery (FBLD). We metabolically label the aromatic amino acids on proteins due to the enrichment of aromatic residues at protein interfaces. We choose the 19F nucleus due to its high signal sensitivity and the hyperresponsiveness of 19F to changes in chemical environment. Simultaneous labeling with two different types of fluorinated aromatic amino acids for PrOF NMR has also been achieved. We first describe the technical aspects of considering the application of PrOF NMR for characterizing native protein-protein interactions and for ligand screening. Several test cases are further described with a focus on a transcription factor coactivator interaction with the KIX domain of CBP/p300 and two epigenetic regulatory domains, the bromodomains of BRD4 and BPTF. Through these case studies, we highlight medicinal chemistry applications in FBLD, selectivity screens, structure-activity relationship (SAR) studies, and ligand deconstruction approaches. These studies have led to the discovery of some of the first inhibitors for BPTF and a novel inhibitor class for the N-terminal bromodomain of BRD4. The speed, ease of interpretation, and relatively low concentration of protein needed for NMR-based binding experiments affords a rapid, structural biology-based method to discover and characterize both native and new ligands for bromodomains, and it may find utility in the study of additional epigenetic proteins and transcription-factor-protein interactions.

Dataset Information

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

Publications

Fragment-Based Ligand Discovery Using Protein-Observed <sup>19</sup>F NMR: A Second Semester Organic Chemistry CURE Project.

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Dataset Information

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

Publications

Fragment-Based Ligand Discovery Using Protein-Observed <sup>19</sup>F NMR: A Second Semester Organic Chemistry CURE Project.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

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