A targeted covalent inhibitor of p97 with proteome-wide selectivity

A resurging interest in targeted covalent inhibitors (TCIs) focus on compounds capable of irreversibly reacting with nucleophilic amino acids in a druggable target. p97 is an emerging protein target for cancer therapy, viral infections and neurodegenerative diseases. Extensive efforts were devoted to the development of p97 inhibitors. The most promising inhibitor of p97 was in phase 1 clinical trials, but failed due to the off-target-induced toxicity, suggesting the selective inhibitors of p97 are highly needed. We report herein a new type of TCIs (i.e., FL-18) that showed proteome-wide selectivity towards p97. Equipped with a Michael acceptor and a basic imidazole, FL-18 showed potent inhibition towards U87MG tumor cells, and in proteome-wide profiling, selectively modified endogenous p97 as confirmed by in situ fluorescence scanning, label-free quantitative proteomics and functional validations. FL-18 selectively modified cysteine residues located within the D2 ATP site of p97. This covalent labeling of cysteine residue in p97 was verified by LC‒MS/MS-based site-mapping and site-directed mutagenesis. Further structure-activity relationship (SAR) studies with FL-18 analogs were established. Collectively, FL-18 is the first known small-molecule TCI capable of covalent engagement of p97 with proteome-wide selectivity, thus providing a promising scaffold for cancer therapy.

Protein targets of medicinally active molecules based on their original structures and molecular probes / 药学学报

Medicinally active molecules are those that have pharmacological effects. Research on protein targets of these molecules not only clarifies their mechanism of action, but also deepens our understanding of biological systems. Here we review recent advances in protein targets of drugs used in clinical practice or in preclinical research. They have various functions including anti-inflammatory, anti-malarial, anti-tumor and other biological activities. Activity-based protein profiling (ABPP) and cellular thermal shift assay (CETSA) are two useful methods to identify the protein targets of small molecules. ABPP depends on a derivative active molecule probe to pull down the protein targets to reveal the interaction mechanisms between the active molecules and targets. Drug target engagement also can be assessed by means of CETSA based on ligand-induced changes in protein thermal stability. In the CETSA approach, the active molecules do not need to be chemically modified. Combining the CETSA method with quantitative mass spectrometry is an effective approach to study the effect of compounds on the thermal profile of a cellular proteome and identify the protein targets. ABPP and CETSA can be complementary and effectively clarify the protein targets. The study of protein targets will help reveal the mechanism of action of medicinal molecules, reveal toxic mechanisms and aid in the discovery of new medicinal targets to promote the process of drug development.

Method and application of proteomics in study of targets of traditional Chinese medicines / 中国中药杂志

The study on the targets of traditional Chinese medicine is an important part of researchers using modern scientific language to clarify the mechanism of traditional Chinese medicine. However, the research on the targets of Chinese medicine is full of challenges due to the complexity of active ingredients. As a branch of systems biology, proteomics focus on specific proteins in living organisms from a holistic perspective, which significantly improves the efficiency of targets discovery and has obvious advantages in the research of targets of Chinese medicine. Based on relevant literature and different methods used in targets of Chinese medicine, proteomics can be divided into chemical proteomics, differential proteomics and quantitative proteomics. The applications of the above three methods are illustrated in this paper as well, which will provide new methods and ideas for the study of the mechanism of Chinese medicine in the future.

Progress in chemical proteomics-based kinome study / 国际药学研究杂志

Protein kinases are key components of cell signaling networks and thereby regulate fundamental biological processes such as cellular growth, proliferation, metabolism and survival. Kinome refers to all kinases in cells or tissue and "kinomics" is the global analysis of kinome with respect to abundance, activity, substrate specificity, phosphorylation pattern and mutational status. Human kinome currently contains 568 members, nearly half of which can be mapped to disease loci and deregulation of kinase activity by gene amplification or mutations has been implicated in diseases such as inflammation, diabetes and cancer. Therefore, human kinome is being recognized as a potentially rich source of drug targets. Kinase inhibitors have been successfully used to treat many kinds of advanced cancers. Chemical proteomics is emerging as a novel comprehensive kinome approach that combines an immobilized inhibitor affinity pull-down approach with mass spectrometry-based proteomics for kinase identification, quantification and phosphorylation analysis under physiological condition. Commonly, one or multiple broad-spectrum kinase inhibitors are covalently immobilized on a biocompatible matrix such as sepharose to enrich all kinases in cells or tissue and then the kinases are identified and quantified by mass spectrometry analysis. It can be used to study the specificity of kinase inhibitor drug, drug candidate or drug resistance mechanism, which can help to understand the mechanism and find combinational drug target. Large-scale unbiased kinome and cancer kinome study will facilitate new drug target discovery and correlate tumor tissue kinome profiles with response to therapy and therefore may be used for future therapy selection in personalized medicine. In this paper, the human kinome, kinase, kinase inhibitor and cancer, chemical proteomics based kinome study progress and its applications in drug discovery are reviewed.

Progress in chemical proteomics-based kinome study / 国际药学研究杂志

Protein kinases are key components of cell signaling networks and thereby regulate fundamental biological processes such as cellular growth, proliferation, metabolism and survival. Kinome refers to all kinases in cells or tissue and “kinomics”is the global analysis of kinome with respect to abundance, activity, substrate specificity, phosphorylation pattern and mutational status. Human kinome currently contains 568 members, nearly half of which can be mapped to disease loci and deregulation of kinase activity by gene amplifica-tion or mutations has been implicated in diseases such as inflammation, diabetes and cancer. Therefore, human kinome is being recognized as a potentially rich source of drug targets. Kinase inhibitors have been successfully used to treat many kinds of advanced cancers. Chemi-cal proteomics is emerging as a novel comprehensive kinome approach that combines an immobilized inhibitor affinity pull-down approach with mass spectrometry-based proteomics for kinase identification, quantification and phosphorylation analysis under physiological condi-tion. Commonly, one or multiple broad-spectrum kinase inhibitors are covalently immobilized on a biocompatible matrix such as sepharose to enrich all kinases in cells or tissue and then the kinases are identified and quantified by mass spectrometry analysis. It can be used to study the specificity of kinase inhibitor drug, drug candidate or drug resistance mechanism, which can help to understand the mechanism and find combinational drug target. Large-scale unbiased kinome and cancer kinome study will facilitate new drug target discovery and correlate tumor tissue kinome profiles with response to therapy and therefore may be used for future therapy selection in personalized medicine. In this paper, the human kinome, kinase, kinase inhibitor and cancer, chemical proteomics based kinome study progress and its applications in drug discovery are reviewed.