Chemoproteomics is a key technology to characterize the mode of action of drugs, as it directly identifies the protein targets of bioactive compounds and aids in the development of optimized small-molecule compounds. Current approaches cannot identify the protein targets of a compound and also detect the interaction surfaces between ligands and protein targets without prior labeling or modification. To address this limitation, we here develop LiP-Quant, a drug target deconvolution pipeline based on limited proteolysis coupled with mass spectrometry that works across species, including in human cells. We use machine learning to discern features indicative of drug binding and integrate them into a single score to identify protein targets of small molecules and approximate their binding sites. We demonstrate drug target identification across compound classes, including drugs targeting kinases, phosphatases and membrane proteins. LiP-Quant estimates the half maximal effective concentration of compound binding sites in whole cell lysates, correctly discriminating drug binding to homologous proteins and identifying the so far unknown targets of a fungicide research compound.

Keywords: Medium rings / Ring contractions / Ring expansion / Sigmatropic rearrangements / ZwitterionsThe bicyclic core of the pumiliotoxins was synthesized in nine to eleven steps starting from L-(−)-proline. This chiral pool starting material was initially converted into an optically active 2-vinylpyrrolidine by standard operations. The first key step allowed the generation of a nine-membered ring lactam by means of a zwitterionic aza-Claisen rearrangement. The 1,4 chirality transfer was found to be low, but the double bond of the azoninone was generated with an exclusive trans configuration in a planar-S arrangement. The mixture of diastereomers thus obtained was immediately epoxid-

The zwitterionic aza-Claisen rearrangement of optically active trans 4-silyloxy-2-vinylpyrrolidines and carboxylic acid fluoride generated nine-membered ring lactams with high yields. The reaction proceeded with an almost complete 1,4-chirality transfer and the exclusive generation of the E-double bond in the medium sized rings to cause additional planar chiral information. The initially formed azoninones were characterized by a pS-arrangement of the olefin with respect to the ring. The rather kinetically stable conformation underwent a flipping of the double bond to give the pR-azoninones as the thermodynamically stable products. The planar diastereomers were subjected to regio- and diastereoselective transannular ring contractions to give indolizidinones. The stereochemical outcome was strongly dependent from the planar chiral information of the double bond and the lactam unit. The so-formed optically active bicycles bearing a defined substitution pattern should serve as versatile building blocks in alkaloid synthesis.

Certain amphibians provide themselves with a chemical defense by accumulating lipophilic alkaloids into skin glands from dietary arthropods. Examples of such alkaloids are pumiliotoxins (PTXs). In general, PTXs are known as positive modulators of voltage-gated sodium channels (VGSCs). Unlike other PTXs, PTX 251D does not share this characteristic. However, mice and insect studies showed that PTX 251D is highly toxic and to date the basis of its toxicity remains unknown. In this work, we searched for the possible target of PTX 251D. The toxin was therefore made synthetically and tested on four VGSCs (mammalian rNa(v)1.2/beta(1), rNa(v)1.4/beta(1), hNa(v)1.5/beta(1) and insect Para/tipE) and five voltage-gated potassium channels (VGPCs) (mammalian rK(v)1.1-1.2, hK(v)1.3, hK(v)11.1 (hERG) and insect Shaker IR) expressed heterologously in Xenopus laevis oocytes, using the two-electrode voltage clamp technique. PTX 251D not only inhibited the Na(+) influx through the mammalian VGSCs but also affected the steady-state activation and inactivation. Interestingly, in the insect ortholog, the inactivation process was dramatically affected. Additionally, PTX 251D inhibited the K(+) efflux through all five tested VGPCs and slowed down the deactivation kinetics of the mammalian VGPCs. hK(v)1.3 was the most sensitive channel, with an IC(50) value 10.8+/-0.5 microM. To the best of our knowledge this is the first report of a PTX affecting VGPCs.

Unsaturated nine-membered ring lactams that contain (E)-olefins within the ring are characterized by planar chiral properties. Thus, selective conversions of the double bond allowed a complete transfer of the planar chiral information into new stereogenic centers The basis of the transformations was the high activation barrier that prevented efficient flipping of the double bond at room temperature (epimerization pR <=> pS) with respect to the ring. Cycloadditions led diastereoselectively to cyclopropano, epimino, epoxy, and dihydroxy azonanones under mild conditions with moderately high yields. The epoxy azonanones were subjected to regio- and diastereoselective transannular epoxide opening/ring contraction sequences to give hydroxy indolizidinones. The regiochemical and stereochemical outcome strongly depends on the configuration of the oxirane and the chiral information of the lactam unit. The so-formed optically active bicycles with defined substitution patterns should serve as versatile building blocks in alkaloid synthesis.