Many therapeutics elicit cell-type specific polypharmacology that is executed by a network of molecular recognition events between a small molecule and the whole proteome. However, measurement of the structures that underpin the molecular associations between the proteome and even common therapeutics, such as the nonsteroidal anti-inflammatory drugs (NSAIDs), is limited by the inability to map the small molecule interactome. To address this gap, we developed a platform termed small molecule interactome mapping by photoaffinity labeling (SIM-PAL) and applied it to the in cellulo direct characterization of specific NSAID binding sites. SIM-PAL uses (1) photochemical conjugation of NSAID derivatives in the whole proteome and (2) enrichment and isotope-recoding of the conjugated peptides for (3) targeted mass spectrometry-based assignment. Using SIM-PAL, we identified the NSAID interactome consisting of over 1000 significantly enriched proteins and directly characterized nearly 200 conjugated peptides representing direct binding sites of the photo-NSAIDs with proteins from Jurkat and K562 cells. The enriched proteins were often identified as parts of complexes, including known targets of NSAID activity (e.g., NF-κB) and novel interactions (e.g., AP-2, proteasome). The conjugated peptides revealed direct NSAID binding sites from the cell surface to the nucleus and a specific binding site hotspot for the three photo-NSAIDs on histones H2A and H2B. NSAID binding stabilized COX-2 and histone H2A by cellular thermal shift assay. Since small molecule stabilization of protein complexes is a gain of function regulatory mechanism, it is conceivable that NSAIDs affect biological processes through these broader proteomic interactions. SIM-PAL enabled characterization of NSAID binding site hotspots and is amenable to map global binding sites for virtually any molecule of interest.

Metabolic chemical reporters of glycosylation in combination with bioorthogonal reactions have been known for two decades and have been used by many different research laboratories for the identification and visualization of glycoconjugates. More recently, however, they have begun to see utility for the investigation of cellular metabolism and the tolerance of biosynthetic enzymes and glycosyltransferases to different sugars. Here, we take this concept one step further by using the metabolic chemical reporter 6-azido-6-deoxy-glucose (6AzGlc). We show that treatment of mammalian cells with the per- O-acetylated version of 6AzGlc results in robust labeling of a variety of proteins. Notably, the pattern of this labeling was consistent with O-GlcNAc modifications, suggesting that the enzyme O-GlcNAc transferase is quite promiscuous for its donor sugar substrates. To confirm this possibility, we show that 6AzGlc-treatment results in the labeling of known O-GlcNAcylated proteins, that the UDP-6AzGlc donor sugar is indeed produced in living cells, and that recombinant OGT will accept UDP-6AzGlc as a substrate in vitro. Finally, we use proteomics to first identify several bona fide 6AzGlc-modifications in mammalian cells and then an endogenous O-glucose modification on host cell factor. These results support the conclusion that OGT can endogenously modify proteins with both N-acetyl-glucosamine and glucose, raising the possibility that intracellular O-glucose modification may be a widespread modification under certain conditions or in particular tissues.

The coxibs are a subset of non-steroidal anti-inflammatory drugs (NSAIDs) that primarily target cyclooxygenase-2 (COX-2) to inhibit prostaglandin signaling and reduce inflammation. However, mechanisms to inhibit other members of the prostaglandin signaling pathway may improve selectivity and reduce off-target toxicity. Here, we report a novel binding site for celecoxib on prostaglandin E synthase (PTGES), an enzyme downstream of COX-2 in the prostaglandin signaling pathway, using a cleavable chelation-assisted biotin probe 6. Evaluation of the multifunctional probe 6 revealed significantly improved tagging efficiencies attributable to the embedded picolyl functional group. Application of the probe 6 within the small molecule interactome mapping by photo-affinity labeling (SIM-PAL) platform using photo-celecoxib as a reporter for celecoxib identified PTGES and other membrane proteins in the top eight enriched proteins from A549 cells. Carbonic anhydrase 12, a known protein target of celecoxib, was also enriched. Four binding sites to photo-celecoxib were additionally mapped by the probe 6, including a binding site with PTGES. The binding interaction with PTGES was validated by competitive displacement with celecoxib and known PTGES inhibitor licofelone. The binding site of photo-celecoxib on PTGES enabled the development of a structural model of the interaction and will inform the design of new selective inhibitors of the prostaglandin signaling pathway. Main textInflammation is a major immune response to injury or infection that leads to short-term symptoms of swelling and pain and, when dysregulated, long-term diseases including arthritis, autoimmune disorders, and neurodegeneration. Induction of the acute inflammatory response is primarily mediated by prostaglandin signaling. 1 The prostaglandins are produced by the cyclooxygenases COX-1 and COX-2, which transform arachidonic acid into prostaglandin H2 (PGH2) for further tailoring by prostaglandin synthases (Figure 1A). The specific inhibition of prostaglandin E2 (PGE2) production and signaling has been an anti-inflammatory target since the development of the first non-steroidal anti-inflammatory drug (NSAID), aspirin, and the subsequent introduction of selective COX-2 inhibitors known as the "coxibs". 2 While therapeutic inhibition of COX-1 and COX-2 is associated with gastrointestinal toxicity, the selective COX-2 inhibitor rofecoxib was withdrawn due to cardiovascular toxicity. 3 This cardiovascular toxicity may arise from the simultaneous suppression of PGE2 and the cardiovascular protectant PGI2 by selective COX-2 inhibitors. 4 As a result, identification of PGE2-selective inhibitors by targeting the inducible prostaglandin E synthase (PTGES) has been the focus of several efforts. [5][6][7][8] Here, we report the discovery of a direct interaction between PTGES and celecoxib using binding site hotspot mapping with an isotopically-coded cleavable chelation-assisted biotin probe (CBPA, 6).Chemical proteomics methods have enabled the unbiased identification of...

An iron complex, tris(4,4′‐bis(hydroxymethyl)‐2,2′‐bipyridine) iron dichloride is reported, which operates at near‐neutral pH with a redox potential of 0.985 V versus SHE. This high potential compound is employed in the posolyte of an aqueous flow battery, paired with bis(3‐trimethylammonio)propyl viologen tetrachloride in the negolyte, exhibiting an open‐circuit voltage of 1.3 V at near‐neutral pH. It demonstrates excellent cycling performance with a low temporal capacity fade rate of 0.07% per day over 35 days of cycling. The extended cycling lifetime is the result of low permeability and improved structural stability of the newly developed iron complex compared to that of the iron tris(bipyridine) complex. The combination of high redox potential and low capacity fade rate compares favorably with those of all previously demonstrated organic and organometallic aqueous posolytes. Extensive investigation into the possible degradation mechanisms, including post‐mortem chemical and electrochemical analyses, indicates that stepwise ligand dissociations of the iron complex are responsible for the reported capacity loss during cell cycling. This investigation provides unprecedented insight to guide further improvements of such metalorganic compounds for energy storage and conversion applications.

We report the synthesis of an electronically-tuned minimally interfering photo-affinity label (MI-PAL), a compact five-carbon tag functionalized with an alkyl diazirine and alkyne handle.