2014. and catalytic domains of Dcp2 with submillimolar affinities. Kinetics analysis revealed that m7GpSpppSm7G is a mixed inhibitor that competes for the Dcp2 active site with micromolar affinity. m7GpSpppSm7G-capped RNA undergoes rapid decapping, suggesting that the compound may act as a tightly bound cap mimic. Our identification of the first small molecule inhibitor of Dcp2 should be instrumental in future studies aimed at understanding the structural basis of RNA decapping and may provide insight toward the development of novel therapeutically relevant decapping inhibitors. Dcp1/2 for either 15 or 30 min in the presence of 200 M nucleotide analog. Capped (m27,3-GpppRNA) and decapped (pRNA) transcripts were resolved by high-resolution SDS-PAGE and quantified by autoradiography. During the reaction, decapped transcripts accumulate and lead to an increase in intensity of the gel band that contains both decapped and uncapped RNA (pppRNA; Fig. 2A; Supplemental Fig. S2B). Open in a separate window FIGURE 2. Decapping inhibition screening assay. (= 0.659). On the other hand, two-headed cap analogs (compounds 12C15) were generally found to be more potent Dcp2 inhibitors (Fig. 2). In particular, the diastereomers of m7GpSppppSm7G, compounds 12a (a mixture of D1 and D2 diastereomers) and 12b (D3 diastereomer), were found to be among the strongest inhibitors within the library (Figs. 2, ?,3).3). The greater inhibitory potency of m7GpS ppppSm7G (D3 diastereomer) (12b) compared to m7GDP (1) or m27,3-GpppG (16) is highly significant (Fig. 2B; Dcp2 and the Dcp1/2 complex with this substrate (Deshmukh et al. 2008; Floor et al. 2010). Fits of Dcp1/2 decapping complex (Ziemniak et al. 2013b). Transcripts containing analogs 12C15 at the 5 terminus were incubated for 15 or 30 min with Dcp1/2, then the reaction Deruxtecan was quenched, and capped versus decapped (and uncapped) transcripts were separated by gel electrophoresis then quantified by autoradiography. The percentage of capped RNA is calculated from the LIPH antibody ratio of capped RNA to the total RNA, and decapping is expressed as the decrease in this percentage (Supplemental Table S6). All RNA transcripts capped with diastereomers of compound 12 were degraded significantly faster than those capped with an unmodified ARCA analog (Fig. 6). This result was surprising since our previous Deruxtecan studies on sulfur-modified cap analogs suggested that introduction of two nonbridging sulfur atoms in the phosphate chain should increase or have a neutral effect on cap analog stability (Grudzien-Nogalska et al. 2007). Cap analog 13, which introduces a methylene bridge into the O-to-S modified two-headed cap, is cleaved from RNA at a rate similar to the unmodified m27,3-band represents capped transcripts whereas band represents a mixture of decapped and uncapped transcripts. (at 4C for 20 min, purified by washing in 70% ethanol and collected again by centrifugation at 9000at 4C for 5 min. The quantity of RNA in the precipitated samples was determined via measurement of Cerenkov radiation in a scintillation counter (Beckman). The samples were resuspended in Deruxtecan Sequencing Gel Loading Buffer (Ambion) and denatured at 95C for 5 min. RNA sequencing gels (10% polyacrylamide) were run at 45C70 W for 3.5 h on a Base Runner Nucleic Acid Sequencer apparatus (International Biotechnologies). Gels were fixed in 5% acetic acid, 5% methanol for 10C15 min, dried onto Whatman 3MM filter paper (Fisher Scientific). Radioactivity in individual bands was quantified by analyzing scanned film using Quantity One program (Bio-Rad). Percentage of inhibition was defined as follows: Single-turnover decapping assays were carried out as previously described (Deshmukh et al. 2008). SpDcp1/21-243 or SpDcp21-243 and inhibitor were combined at 3 concentration in the decapping reaction buffer (50 mM TrisCCl [pH 8 at 25C], 50 mM NH4Cl, 0.01% NP-40, 1 mM DTT, and 5 mM MgCl2). The decapping reaction was initiated by adding 30 L capped 32P-labeled 29 nt RNA substrate at 1.5 concentration in decapping reaction buffer to 60 L 3 protein + inhibitor at 4C. Final protein concentrations ranged from 0.8C25 M; final inhibitor concentrations ranged from 0.03C1 mM; final RNA concentration was 100 pM. Time points were quenched by addition of excess EDTA, RNA was separated from m7GDP product by thin layer chromatography, and the fraction of capped versus decapped transcripts was quantified using a GE Typhoon scanner and ImageQuant as previously described (Deshmukh et al. 2008). Plots of fraction m7GDP product versus time were fit to a first order exponential to extract em k /em obs; plots of em k /em obs versus enzyme concentration were fit to the MichaelisCMenten equation: em k /em obs = em k /em max[E]/ em K /em M + [E], to extract em k /em max and em K /em M. em Measuring kinetic constants with inhibitor 12b /em . em K /em Mapp and.