Chemical biology of antigen presentation by MHC molecules

Bio-organic Synthesi

Spatially resolved sampling for untargeted metabolomics: a new tool for salivomics

Saliva is a complex bodily fluid composed of metabolites secreted by major and minor glands, as well as by-products of host oral cells, oral bacteria, gingival crevicular fluid, and exogenous compounds. Major salivary glands include the paired parotid, submandibular, and sublingual glands. The secreted fluids of the salivary glands vary in composition, flow rate, site of release, and clearance suggesting that different types of saliva fulfill different functions and therefore can provide unique biological information. Consequently, for the comprehension of the functionality of the salivary components, spatially resolved investigations are warranted. To understand and comprehensively map the highly heterogeneous environment of the oral cavity, advanced spatial sampling techniques for metabolomics analysis are needed. Here, we present a systematic evaluation of collection devices for spatially resolved sampling aimed at untargeted metabolomics and propose a comprehensive and reproducible collection and analysis protocol for the spatially resolved analysis of the human oral metabolome.Proteomic

Drug Discovery Maps, a Machine Learning Model That Visualizes and Predicts Kinome-Inhibitor Interaction Landscapes

The interpretation of high-dimensional structure-activity data sets in drug discovery to predict ligand-protein interaction landscapes is a challenging task. Here we present Drug Discovery Maps (DDM), a machine learning model that maps the activity profile of compounds across an entire protein family, as illustrated here for the kinase family. DDM is based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm to generate a visualization of molecular and biological similarity. DDM maps chemical and target space and predicts the activities of novel kinase inhibitors across the kinome. The model was validated using independent data sets and in a prospective experimental setting, where DDM predicted new inhibitors for FMS-like tyrosine kinase 3 (FLT3), a therapeutic target for the treatment of acute myeloid leukemia. Compounds were resynthesized, yielding highly potent, cellularly active FLT3 inhibitors. Biochemical assays confirmed most of the predicted off-targets. DDM is further unique in that it is completely open-source and available as a ready-to-use executable to facilitate broad and easy adoption

Doxorubicin and aclarubicin: shuffling anthracycline glycans for improved anticancer agents

Anthracycline anticancer drugs doxorubicin and aclarubicin have been used in the clinic for several decades to treat various cancers. Although closely related structures, their molecular mode of action diverges, which is reflected in their biological activity profile. For a better understanding of the structure-function relationship of these drugs, we synthesized ten doxorubicin/aclarubicin hybrids varying in three distinct features: aglycon, glycan, and amine substitution pattern. We continued to evaluate their capacity to induce DNA breaks, histone eviction, and relocated topoisomerase II alpha in living cells. Furthermore, we assessed their cytotoxicity in various human tumor cell lines. Our findings underscore that histone eviction alone, rather than DNA breaks, contributes strongly to the overall cytotoxicity of anthracyclines, and structures containing N,N-dimethylamine at the reducing sugar prove that are more cytotoxic than their nonmethylated counterparts. This structural information will support further development of novel anthracycline variants with improved anticancer activity.Bio-organic Synthesi

Re-exploring the anthracycline chemical space for better anti-cancer compounds

The anthracycline anti-cancer drugs are intensely usedin the clinicto treat a wide variety of cancers. They generate DNA double strandbreaks, but recently the induction of chromatin damage was introducedas another major determinant of anti-cancer activity. The combinationof these two events results in their reported side effects. Whileour knowledge on the structure-activity relationship of anthracyclineshas improved, many structural variations remain poorly explored. Therefore,we here report on the preparation of a diverse set of anthracyclineswith variations within the sugar moiety, amine alkylation pattern,saccharide chain and aglycone. We assessed the cytotoxicity in vitro in relevant human cancer cell lines, and the capacityto induce DNA- and chromatin damage. This coherent set of data allowedus to deduce a few guidelines on anthracycline design, as well asdiscover novel, highly potent anthracyclines that may be better toleratedby patients.Bio-organic Synthesi

Immunoproteasome inhibitor-doxorubicin conjugates target multiple myeloma cells and release doxorubicin upon low-dose photon irradiation

Proteasome inhibitors are established therapeutic agents for the treatment of hematological cancers, as are anthracyclines such as doxorubicin. We here present a new drug targeting approach that combines both drug classes into a single molecule. Doxorubicin was conjugated to an immunoproteasome-selective inhibitor via light-cleavable linkers, yielding peptide epoxyketone-doxorubicin prodrugs that remained selective and active toward immunoproteasomes. Upon cellular uptake and immunoproteasome inhibition, doxorubicin is released from the immunoproteasome inhibitor through photoirradiation. Multiple myeloma cells in this way take a double hit: immunoproteasome inhibition and doxorubicin-induced toxicity. Our strategy, which entails targeting of a cytotoxic agent, through a covalent enzyme inhibitor that is detrimental to tumor tissue in its own right, may find use in the search for improved anticancer drugs.ERC-2014-StG-639005Bio-organic Synthesi

Synthetic (N,N-dimethyl)doxorubicin glycosyl diastereomers to dissect modes of action of anthracycline anticancer drugs

Bio-organic Synthesi

Reciprocal chemical genetics for swift lead and target identification

Bio-Organische synthes

A brief report on combination chemotherapy and anti-programmed death (ligand) 1 treatment in small-cell lung cancer: did we choose the optimal chemotherapy backbone?

Extensive-stage small-cell lung cancer (ES-SCLC) is an aggressive cancer that remains very hard to treat. The life expectancy of a patient diagnosed with this disease has not changed over the past three decades. Recently, three large clinical studies showed a survival benefit by adding an anti-programmed death (ligand) 1 (PD-(L) 1 antibody to the current chemotherapy regimen. Although significant and important, the benefit seems less than what has been achieved in patients with non-small-cell lung cancer treated with chemoimmunotherapy. A number of hypotheses have been explored to explain this discrepancy. Here, we hypothesise that the current chemotherapy backbone in ES-SCLC does not contain the optimal drugs to trigger immunogenic cell death and therefore does not induce a synergy between chemotherapy and immune checkpoint inhibitor therapy. Thereby, we advocate that doxorubicin treatment instead of etoposide should be reconsidered as standard-of-care (SoC) first-line treatment of SCLC. (c) 2020 Published by Elsevier Ltd

A trimeric Rab7 GEF controls NPC1-dependent lysosomal cholesterol export

Cholesterol import in mammalian cells is mediated by the LDL receptor pathway. Here, we perform a genome-wide CRISPR screen using an endogenous cholesterol reporter and identify >100 genes involved in LDL-cholesterol import. We characterise C18orf8 as a core subunit of the mammalian Mon1-Ccz1 guanidine exchange factor (GEF) for Rab7, required for complex stability and function. C18orf8-deficient cells lack Rab7 activation and show severe defects in late endosome morphology and endosomal LDL trafficking, resulting in cellular cholesterol deficiency. Unexpectedly, free cholesterol accumulates within swollen lysosomes, suggesting a critical defect in lysosomal cholesterol export. We find that active Rab7 interacts with the NPC1 cholesterol transporter and licenses lysosomal cholesterol export. This process is abolished in C18orf8-, Ccz1- and Mon1A/B-deficient cells and restored by a constitutively active Rab7. The trimeric Mon1-Ccz1-C18orf8 (MCC) GEF therefore plays a central role in cellular cholesterol homeostasis coordinating Rab7 activation, endosomal LDL trafficking and NPC1-dependent lysosomal cholesterol export. Lysosomes play an important role in cellular LDL-cholesterol uptake. Here, the authors perform a genome-wide genetic screen for cholesterol regulators and identify C18orf8 as a conserved subunit of a trimeric Rab7 GEF that controls LDL trafficking and NPC1-dependent lysosomal cholesterol export