Adaptive resistance of myeloma to proteasome inhibition represents a clinical challenge, whose biology is poorly understood. Proteasome mutations were implicated as underlying mechanism, while an alternative hypothesis based on low activation status of the unfolded protein response was recently suggested (IRE1/XBP1-low model). We generated bortezomib- and carfilzomib-adapted, highly resistant multiple myeloma cell clones (AMO-BTZ, AMO-CFZ), which we analyzed in a combined quantitative and functional proteomic approach. We demonstrate that proteasome inhibitor-adapted myeloma cells tolerate subtotal proteasome inhibition, irrespective of a proteasome mutation, and uniformly show an 'IRE1/XBP1-low' signature. Adaptation of myeloma cells to proteasome inhibitors involved quantitative changes in >600 protein species with similar patterns in AMO-BTZ and AMO-CFZ cells: proteins involved in metabolic regulation, redox homeostasis, and protein folding and destruction were upregulated, while apoptosis and transcription/translation were downregulated. The quantitatively most upregulated protein in AMO-CFZ cells was the multidrug resistance protein (MDR1) protein ABCB1, and carfilzomib resistance could be overcome by MDR1 inhibition. We propose a model where proteasome inhibitor-adapted myeloma cells tolerate subtotal proteasome inhibition owing to metabolic adaptations that favor the generation of reducing equivalents, such as NADPH, which is supported by oxidative glycolysis. Proteasome inhibitor resistance may thus be targeted by manipulating the energy and redox metabolism.

The close interaction between organic chemi stry and biology goes back to the late 18th century, when the modern natural sciences began to take shape. After synthetic organic chemistry arose as a discipline, organic chemists almost immediately began to pursue the synthesis of naturally occurring compounds, thereby contributing to the understanding of their functions in biological processes. Research in those days was often remarkably interdisciplinary; in fact, it constituted chemical biology research before the phrase even existed. For example, histological dyes, both of an organic and inorganic nature, were developed and applied by independent researchers (Gram and Golgi) with the aim of visualizing cellular substructures (the bacterial cell wall and the Golgi apparatus).Over the years, as knowledge within the various fields of the natural sciences deepened, research disciplines drifted apart, becoming rather monodisciplinary. In these years, broadly ranging from the end of World War II to about the 1980s, organic chemistry continued to impact life sciences research, but contributions were of a more indirect nature. As an example, the development of the polymerase chain reaction, from which molecular biology and genetics research have greatly profited, was partly predicated on the availability of synthetic oligonucleotides. These molecules first became available in the late 1960s, the result of organic chemists pursuing the synthesis of DNA oligomers primarily because of the synthetic challenges involved.Today, academic natural sciences research is again becoming more interdisciplinary, and sometimes even multidisciplinary. What was termed “chemical biology” by Stuart Schreiber at the end of the last century can be roughly described as the use of intellectually chemical approaches to shed light on processes that are fundamentally rooted in biology. Chemical tools and techniques that are developed for biological studies in the exciting and rapidly evolving field of chemical biology research include contributions from many areas of the multifaceted discipline of chemistry, and particularly from organic chemistry. Researchers apply knowledge inherent to organic chemistry, such as reactivity and selectivity, to the manipulation of specific biomolecules in biological samples (cell extracts, living cells, and sometimes even animal models) to gain insight into the biological phenomena in which these molecules participate.In this Account, we highlight some of the recent developments in chemical biology research driven by organic chemistry, with a focus on bioorthogonal chemistry in relation to activity-based protein profiling. The rigorous demands of bioorthogonality have not yet been realized in a truly bioorthogonal reagent pair, but remarkable progress has afforded a range of tangible contributions to chemical biology research. Activity-based protein profiling, which aims to obtain information on the workings of a protein (or protein family) within the larger context of the full biological system, has in particular benefited from these advances. Both activity-based protein profiling and bioorthogonal chemistry have been around for approximately 15 years, and about 8 years ago the two fields very profitably intersected. We expect that each discipline, both separately and in concert, will continue to make important contributions to chemical biology research.

Epithelial cells of the thymus cortex express a unique proteasome particle involved in positive T cell selection. This thymoproteasome contains the recently discovered β5t subunit that has an uncharted activity, if any. We synthesized fluorescent epoxomicin probes that were used in a chemical proteomics approach, entailing activity-based profiling, affinity purification, and LC-MS identification, to demonstrate that the β5t subunit is catalytically active in the murine thymus. A panel of established proteasome inhibitors showed that the broad-spectrum inhibitor epoxomicin blocks the β5t activity and that the subunit-specific antagonists bortezomib and NC005 do not inhibit β5t. We show that β5t has a substrate preference distinct from β5/β5i that might explain how the thymoproteasome generates the MHC class I peptide repertoire needed for positive T cell selection.Highlights► Activity-based profiling with fluorescent epoxomicin shows a new band in murine thymus ► LC-MS3 analysis identified this activity as the thymoproteasome-specific β5t subunit β5t prefers a hydrophilic residue in a hydrophobic stretch shown by competitive ABP ► Thus, β5t is actively involved in positive T cell selection.

Chitosan is a biocompatible polysaccharide of natural origin that can act as a permeation enhancer. In this study, we used an integral in vitro/in vivo correlation approach to: a) investigate polysaccharide-mediated absorption kinetics of the peptide drug octreotide across mammalian airway epithelium, b) assess formulation toxicity, c) correlate the mechanism of permeation enhancement. The 20% and 60% N-trimethylated chitosan derivatives (TMC20 and TMC60) were synthesized by alkaline methylation using chitosan as starting material. Octreotide was administered in control buffers or in 1.5% (w/v) gel-phase formulations of pH 5.5 for chitosan and pH 7.4 for TMCs. In vitro, reconstituted Calu-3 cell monolayers were used for trans-epithelial electrical resistance (TEER), transport and cytotoxicity assays. Intratracheal instillation in rats was used to determine octreotide kinetics and formulation toxicity in vivo.Chitosan, TMC20 and TMC60 decreased TEER significantly and enhanced octreotide permeation in vitro by 21-, 16- and 30-fold. In vivo, sustained release properties of the formulations were observed and the bio-availability was enhanced by 2.4-, 2.5- and 3.9-fold, respectively. Interestingly, we found a linear in vitro/in vivo correlation between calculated absorption rates (R2 = 0.93), suggesting that the permeation enhancement by polysaccharides, both in vitro and in vivo, proceeds via an analogous mechanism. Cell viability and histology studies showed that the TMCs are safer than chitosan and that Calu-3 cell monolayers are a valuable model for predicting paracellular transport kinetics in airway epithelia. Additionally, cationic polysaccharides are promising enhancers for peptide drug absorption with prospect for sustained-release formulations.