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Sphingolipid metabolism plays an important role in determining the fate of a cell. Among several sphingolipid metabolites, ceramide is a key player in intracellular signal transduction. Ceramide is usually converted to various metabolites such as sphingomyelin, sphingosine, ceramide-1-phosphate, and glucosylceramide. If ceramide is accumulated in the cell, it induces apoptosis. On the other hand, its metabolite sphingosine is converted to sphingosine-1-phosphate (S1P), which promotes angiogenesis via G protein coupled receptor signaling. Therefore, the equilibrium in ceramide and S1P levels in cells plays an important role in angiogenesis as well as cell death. Acid ceramidase (AC) is a promising target protein in the development of multi-targeted anticancer drugs as its inhibition can simultaneously inhibit angiogenesis via the Akt and ERK 1/2 pathway and limit cancer growth through ceramide-induced apoptosis. Although some inhibitors of AC have been reported, they have not been proven effective for human therapy. Recent advancement in the elucidation of AC structure will facilitate the development of better inhibitors for treating human diseases.

Antiangiogenesis is now thought of as one of the most important approaches for anticancer therapy. In this study, we determined the antiangiogenic property of herboxidiene, a polyketide natural product. Herboxidiene effectively inhibited the proliferation of human umbilical vein endothelial cells (HUVECs) at concentrations not exhibiting cytotoxicity. Furthermore, the natural product significantly suppressed vascular endothelial growth factor-induced invasion and tube formation in HUVECs as well as neovascularization of the chorioallantoic membrane in developing chick embryos. We also identified an association between the antiangiogenic activity of herboxidiene and the downregulation of both the phosphorylation of VEGF receptor 2 (KDR/Flk-1) and the expression of hypoxia-inducible factor-1α at the transcriptional level. These results suggest that herboxidiene functions as a potential antiangiogenic agent and may be applicable for anticancer therapy by targeting tumor angiogenesis.

MALDI mass spectrometry imaging (MSI) provides a technology platform that allows the accurate visualization of unlabeled small molecules within the two-dimensional spaces of tissue samples. MSI has proven to be a powerful tool-box concept in the development of new drugs. MSI allows unlabeled drug compounds and drug metabolites to be detected and identified and quantified according to their mass-to-charge ratios (m/z) at high resolution in complex tissue environments. Such drug characterization in situ, by both spatial and temporal behaviors within tissue compartments, provide new understandings of the dynamic processes impacting drug uptake and metabolism at the local sites targeted by therapy. Further, MSI in combination with histology and immunohistochemistry, provides the added value of defining the context of cell biology present at the sites of drug localization thus providing invaluable information relating to treatment efficacy. In this report we provide mass spectrometry imaging data within various cancers such as malignant melanoma in patients administered with vemurafenib, a protein kinase inhibitor that is targeting BRAF mutated proteins and that has shown significant efficacy in restraining disease progression. We also provide an overview of other examples of the new generation of targeted drugs, and demonstrate the data on personalized medicine drugs localization within tumor compartments within in vivo models. In these cancer models we provide detailed data on drug and target protein co-localization of YCG185 and sunitinib. These drugs are targeting VEGFR2 within the angiogenesis mechanism. Our ability to resolve drug uptake at targeted sites of directed therapy provides important opportunities for increasing our understanding about the mode of action of drug activity within the environment of disease.

Identification of the target proteins of bioactive small molecules isolated from phenotypic screens plays an important role in chemical biology and drug discovery. However, discovering the targets of small molecules is often the most challenging and time-consuming step for chemical biology researchers. To overcome the bottlenecks in target identification, many new approaches based on genomics, proteomics, and bioinformatics technologies have been developed. Here, we provide an overview of the current major methodologies for target deconvolution of bioactive small molecules. To obtain an integrated view of the mechanisms of action of small molecules, we propose a systematic approach that involves the combination of multi-omics-based target identification and validation and preclinical target validation.

Autophagy is the mass degradation system that removes long-lived proteins and malfunctioning organelles within the cell. Dysfunctional autophagic processes can cause various diseases such as cancer and neurodegenerative disorders, but the underlying mechanisms responsible for such events remain undefined. Small molecules that control autophagy could be powerful tools to reveal autophagy mechanisms, and to develop treatments for autophagy-related diseases including Alzheimer’s disease, Parkinson’s disease and various cancer types. This review discusses the small molecules that have been identified to control autophagy and how they can be used to understand signaling pathways important for autophagy in the context of chemical genomics.