Nucleotide-sugar donors containing bioorthogonal moieties are important tools to study cellular glycosylation. Typically, the acetamide moiety in N-acetylhexosamines such as GlcNAc and GalNAc is replaced by an acylamide with a clickable tag and converted to the corresponding uridine diphosphate analogue. These probes can then be tested for acceptance by glycosyltransferase enzymes in vitro. Lengthy procedures in synthetic chemistry currently limit the availability of bioorthogonal uridine diphosphate (UDP)-sugar analogues. Chemoenzymatic synthesis has proven to be a powerful and effective alternative, and multiple approaches have been published to date. In this protocol, we describe a streamlined method for the generation of bioorthogonal UDP-GlcNAc and UDP-GalNAc analogues. We describe the chemical modification of D-glucosamine and D-galactosamine to incorporate bioorthogonal acylamides, the subsequent one-pot multienzyme conversion to the corresponding UDP-sugar analogues, and reproducible purification. Our approach features the bacterial kinase NahK and human pyrophosphorylase AGX1 as well as a recombinantly expressed AGX1 variant with an expanded substrate profile. The approach further features an inorganic pyrophosphatase and an alkaline phosphatase to improve enzymatic turnover and aid the purification process, respectively. The use of biosynthetic enzymes with substrate promiscuity extends the scope of bioorthogonal nucleotide-sugar analogue structures to aid efforts in chemical glycobiology. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Chemical synthesis of bioorthogonally tagged acylamide analogues of D-GlcNAc and D-GalNAc Alternate Protocol 1: Chemical synthesis of bioorthogonally tagged acylamide analogues of D-GlcNAc and D-GalNAc from a protected GlcNH2 or GalNH2 precursor Basic Protocol 2: Conversion of D-GlcNAc or D-GalNAc analogues to UDP-sugars using analytical- (reaction scouting) and preparative-scale enzymatic synthesis and purification.
Targeted protein degradation using bifunctional molecules like proteolysis targeting chimeras (PROTACs) has revolutionized drug discovery but remains limited by E3 ligase availability and lack of cell selectivity. N-degron degraders provide a smaller, more drug-like alternative that harnesses endogenous N-terminal degradation signals independent of recruited ligases. However, they are prone to proteolysis and lack mechanisms for tissue-specific activation. To overcome these challenges, we developed a "caged" N-degron degrader selectively activated by the immunoproteasome (iCP), a proteasome isoform induced in cancer and inflammatory settings. By appending an iCP-recognition tetrapeptide (Ala-Thr-Met-Trp) capped with a morpholine group to the N-terminus, we shielded the degron from nonspecific cleavage and enabled selective activation in iCP-expressing cells. This design improved stability, enhanced degradation potency, and minimized activity in healthy cells. Our findings establish a generalizable strategy to spatially control N-degron activity through disease-specific proteolytic environments, advancing safer and more selective protein degradation therapeutics. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and characterization of an N-degron degrader for Abl Basic Protocol 2: Synthesis and characterization of an immunoproteasome N-degron prodrug Basic Protocol 3: Assessing protein degradation in cells.
Small molecule microarray (SMM) technology has become a powerful tool used in high-throughput screening for target-based drug discovery. One area in which SMMs have found use is the identification of small molecule ligands for RNA. RNAs with unique secondary or tertiary three-dimensional structures are considered to be attractive targets for small molecules. Complex RNA structures can form hydrophobic pockets suitable for small molecule binding, representing an opportunity for developing novel therapeutics. Our lab has previously taken a target-based approach, screening a single target against many small molecules on an SMM platform. Here, we report a screening protocol for SMMs to investigate multiple RNAs simultaneously using multi-color imaging. By introducing a mixture containing different fluorophore-labeled RNAs, the fluorescence signal of each binding event can be observed simultaneously. Thus, the specificity of a hit compound binding to one RNA target over other highly abundant RNAs (such as tRNA or rRNA) can be easily evaluated. © 2020 Wiley Periodicals LLC. Basic Protocol: RNA screening on SMMs by multi-color imaging Support Protocol 1: Preparation of SMM slides Support Protocol 2: Fluorophore labeling of RNA through maleimide chemistry.
Reversible addition-fragmentation chain-transfer (RAFT) polymerization is a commonly used polymerization methodology to generate synthetic polymers. The products of RAFT polymerization, i.e., RAFT polymers, have been widely employed in several biologically relevant areas, including drug delivery, biomedical imaging, and tissue engineering. In this article, we summarize a synthetic methodology to display an azide group at the chain end of a RAFT polymer, thus presenting a reactive site on the polymer terminus. This platform enables a click reaction between azide-terminated polymers and alkyne-containing molecules, providing a broadly applicable scaffold for chemical and bioconjugation reactions on RAFT polymers. We also highlight applications of these azide-terminated RAFT polymers in fluorophore labeling and for promoting organelle targeting capability. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Synthesis of the azide derivatives of chain transfer agent and radical initiator Basic Protocol 2: Installation of an azide group on the α-end of RAFT polymers Alternate Protocol: Installation of an azide group on the ω-end of RAFT polymers Basic Protocol 3: Click reaction between azide-terminated RAFT polymers and alkyne derivatives.
Drug-induced liver injury is an important cause of non-approval in drug development and the withdrawal of already approved drugs from the market. Screening human hepatic cell lines for toxicity has been used extensively to predict drug-induced liver injury in preclinical drug development. Assessing hepatic-cell health with more diverse markers will increase the value of in vitro assays and help predict the mechanism of toxicity. We describe three live cell-based assays using HepG2 cells to measure cell health parameters indicative of hepatotoxicity. The first assay measures cellular ATP levels using luciferase. The second and third assays are multiparametric high-content screens covering a panel of cell health markers including cell count, mitochondrial membrane potential and structure, nuclear morphology, vacuolar density, and reactive oxygen species and glutathione levels. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Measurement of cellular ATP content Basic Protocol 2: High-content analysis assay to assess cell count, mitochondrial membrane potential and structure, and reactive oxygen species Basic Protocol 3: High-content analysis assay to assess nuclear morphology, vacuoles, and glutathione content Support Protocol 1: Subculturing and maintaining HepG2 cells Support Protocol 2: Plating HepG2 cell line Support Protocol 3: Transferring compounds by pin tool Support Protocol 4: Generating dose-response curves.
