Identifying drug targets with thermal proteome profiling using IBT-16plex

RATIONALE

Thermal proteome profiling (TPP) has been widely used for the identification of drug targets for several years, and TMTpro-16plex has recently been evaluated for TPP of vehicle- and drug-treated samples in a single labeling process to reduce missing values and save instrument time. A novel isobaric labeling reagent, IBT-16plex, was developed with slightly better performance in protein identification and quantification than the commercially available TMTpro-16plex.

METHODS

In this study, we applied the newly developed IBT-16plex for target identification of methotrexate and panobinostat using TPP.

RESULTS

The known targets of these two drugs were successfully identified with elevated melting temperatures, and some known off-targets and potential new off-targets were also identified.

CONCLUSIONS

IBT-16plex can be a cost-effective replacement for TMTpro-16plex for TPP applications.

A clickable photoaffinity probe of betulinic acid identifies tropomyosin as a target

Target identification of bioactive compounds is important for understanding their mechanisms of action and provides critical insights into their therapeutic utility. While it remains a challenge, unbiased chemoproteomics strategy using clickable photoaffinity probes is a useful and validated approach for target identification. One major limitation of this approach is the efficient synthesis of appropriately substituted clickable photoaffinity probes. Herein, we describe an efficient and consistent method to prepare such probes. We further employed this method to prepare a highly stereo-congested probe based on naturally occurring triterpenoid betulinic acid. With this photoaffinity probe, we identified tropomyosin as a novel target for betulinic acid that can account for the unique biological phenotype on cellular cytoskeleton induced by betulinic acid.

Orthogonal Design of Supramolecular Prodrug Vesicles via Water-Soluble Pillar[5]arene and Betulinic Acid Derivative for Dual Chemotherapy

Supramolecular prodrug vesicles with efficient property for dual chemotherapy have been successfully constructed based on the orthogonal self-assembly between a water-soluble pillar[5]arene host (WP5) and a betulinic acid guest (BA-D) as well as doxorubicin (DOX). Under the acidic microenvironment of cancer cells, both the encapsulated anticancer drug DOX and prodrug BA-D can be effectively released from DOX-loaded WP5⊃BA-D prodrug vesicles for combinational chemotherapy. Furthermore, bioexperiments indicate that DOX-loaded prodrug vesicles can obviously enhance the anticancer efficiency based on the cooperative effect of DOX and BA-D, while remarkably reducing the systematic toxicity in tumor-mice, displaying great potential applications in combinational chemotherapy for cancer treatments.

Photoaffinity-Based Chemical Proteomics Reveals 7-Oxocallitrisic Acid Targets CPT1A to Trigger Lipogenesis Inhibition

One of the natural terpenoids isolated from Resina Commiphora, 7-oxocallitrisic acid (7-OCA), has lipid metabolism regulatory activity. To uncover its lipogenesis inhibition mechanism, we developed a photoaffinity and clickable probe based on the 7-OCA scaffold and performed chemical proteomics to profile its potential cellular targets. It was found that 7-OCA could directly interact with carnitine palmitoyl transferase 1A (CPT1A) to promote its activity to reduce lipid accumulation. The present work reveals our understanding of the mode of lipid mebabolism regulation by abietic acids and provides new clues for antiobesity drug development with CPT1A as a main target.

Currently Available Strategies for Target Identification of Bioactive Natural Products

In recent years, biologically active natural products have gradually become important agents in the field of drug research and development because of their wide availability and variety. However, the target sites of many natural products are yet to be identified, which is a setback in the pharmaceutical industry and has seriously hindered the translation of research findings of these natural products as viable candidates for new drug exploitation. This review systematically describes the commonly used strategies for target identification via the application of probe and non-probe approaches. The merits and demerits of each method were summarized using recent examples, with the goal of comparing currently available methods and selecting the optimum techniques for identifying the targets of bioactive natural products.

Target identification of anticancer natural products using a chemical proteomics approach

In recent years, there has been a strong demand worldwide for the identification and development of potential anticancer drugs based on natural products. Natural products have been explored for their diverse biological and therapeutic applications from ancient time. In order to enhance the efficacy and selectivity and to minimize the undesired side effects of anti cancer natural products (ANPs), it is essential to understand their target proteins and their mechanistic pathway. Chemical proteomics is one of the most powerful tools to connect ANP target identification and quantification where labeling and non-labeling based approaches have been used. Herein, we have discussed the various strategies to systemically develop selective ANP based chemical probes to characterise their specific and non-specific target proteins using a chemical proteomic approach in various cancer cell lysates.

Development and application of novel electrophilic warheads in target identification and drug discovery

Nucleophilic amino acids play important roles in maintenance of protein structure and function, covalent modification of such amino acid residues by therapeutic agents is an efficient way to treat human diseases. Most of current clinical drugs are structurally limited to α,β-unsaturated amide as an electrophilic warhead. To alleviate this issue, many novel electrophiles have been developed in recent years that can covalently bind to different amino acid residues and provides a unique way to interrogate proteins, including "undruggable" targets. With an activity-based protein profiling (ABPP) approach, the activity and functionality of a protein and its binding sites can be assessed. This facilitates an understanding of protein function, and contributes to the discovery of new druggable targets and lead compounds. Meanwhile, many novel inhibitors bearing new reactive warhead were developed and displayed remarkable pharmaceutical properties. In this perspective, we have reviewed the recent remarkable progress of novel electrophiles and their applications in target identification and drug discovery.

Harnessing affinity-based protein profiling to reveal a novel target of nintedanib

Nintedanib (BIBF1120), a triple angiokinase inhibitor, was first approved for idiopathic pulmonary fibrosis (IPF) therapy and is also efficacious for lung carcinoma, and interstitial lung diseases, far beyond its inhibition of VEGFR/PDGFR/FGFR. We identified tripeptidyl-peptidase 1 (TPP1) as one of the direct targets of nintedanib employing the affinity-based protein profiling (AfBPP) technique. This may be a new mechanism for nintedanib's role different from tyrosine kinase inhibition.

Target identification of natural medicine with chemical proteomics approach: probe synthesis, target fishing and protein identification

Natural products are an important source of new drugs for the treatment of various diseases. However, developing natural product-based new medicines through random moiety modification is a lengthy and costly process, due in part to the difficulties associated with comprehensively understanding the mechanism of action and the side effects. Identifying the protein targets of natural products is an effective strategy, but most medicines interact with multiple protein targets, which complicate this process. In recent years, an increasing number of researchers have begun to screen the target proteins of natural products with chemical proteomics approaches, which can provide a more comprehensive array of the protein targets of active small molecules in an unbiased manner. Typically, chemical proteomics experiments for target identification consist of two key steps: (1) chemical probe design and synthesis and (2) target fishing and identification. In recent decades, five different types of chemical proteomic probes and their respective target fishing methods have been developed to screen targets of molecules with different structures, and a variety of protein identification approaches have been invented. Presently, we will classify these chemical proteomics approaches, the application scopes and characteristics of the different types of chemical probes, the different protein identification methods, and the advantages and disadvantages of these strategies.

Quantitative Proteomics Reveals Cellular Off-Targets of a DDR1 Inhibitor

Target identification of small molecules is a great challenge but an essential step in drug discovery. Here, a quantitative proteomics approach has been used to characterize the cellular targets of DR, a DDR1 inhibitor. By taking advantage of competitive affinity-based protein profiling coupled with bioimaging, Cathepsin D (CTSD) was found to be the principle off-target of DR in human cancer cells. Further findings suggest the potential of DR as a novel CTSD inhibitor for breast cancer treatment. In addition, a trans-cyclooctene (TCO) containing probe was developed to track the binding between DR and its target proteins in living systems and could be a useful tool for DDR1 detection.

Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors

Affinity-based protein profiling has proven to be a powerful method in target identification of bioactive molecules. Here, this technology was applied in two photoreactive anticancer inhibitors, arenobufagin and HM30181. Using UV irradiation, these photoreactive reagents can covalently cross-link to target proteins, leading to a covalent binding with target proteins. Moreover, the cellular on/off targets of these two molecules, including ATP1A1, MDR1, PARP1, DDX5, NOP2, RAB6A, and ERGIC1 were first identified by affinity-based protein profiling and bioimaging approaches. The protein hit, PARP1, was further validated to be involved in the function of the anticancer effects.

Applications of Activity-Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery

Activity-based protein profiling (ABPP) and bioimaging have been developed in recent years as powerful technologies in drug discovery. Specifically, both approaches can be applied in critical steps of drug development, such as therapy target discovery, high-throughput drug screening and target identification of bioactive molecules. We have been focused on the development of various strategies that enable simultaneous activity-based protein profiling and bioimaging studies, thus facilitating an understanding of drug actions and potential toxicities. In this Minireview, we summarize these novel strategies and applications, with the aim of promoting these technologies in drug discovery.

Expanding the "minimalist" small molecule tagging approach to different bioactive compounds

"Minimalist" small molecule tagging (MSMT) is a promising approach that easily converts bioactive compounds into affinity-based probes (AfBPs) for proteomic studies. In this work, seven bioactive compounds targeting diversified protein classes were installed with "minimalist" linkers through common reactions to generate the corresponding AfBPs. These probes were evaluated for cell-based protein profiling and target validation. Among them, the entinostat-derived probe EN and the camptothecin-derived probe CA were further utilized in cellular imaging and SILAC-based large-scale target identification. Our extensive studies suggest that the "minimalist" small molecule tagging approach could be expanded to different classes of bioactive compounds for modification into AfBPs as a dual functional tool for both proteomics and cellular imaging.

Activity-based protein profiling reveals that secondary-carbon-centered radicals of synthetic 1,2,4-trioxolanes are predominately responsible for modification of protein targets in malaria parasites

Endoperoxide-containing antimalarials, such as artemisinin and the synthetic trioxolane OZ439, are prodrugs activated by heme to generate primary and secondary carbon-centered radicals. We employed activity-based protein profiling (ABPP) to show that the secondary-carbon-centered radical of 1,2,4-trioxolanes is primarily responsible for protein labeling in malaria parasites.

Crenolanib-Derived Probes Suitable for Cell- and Tissue-Based Protein Profiling and Single-Cell Imaging

Crenolanib (CP-868,596), a potent inhibitor of FLT3 and PDGFRα/β, is currently under phase III clinical investigation for the treatment of acute myeloid leukemia. However, the protein targets of Crenolanib in cancer cells remain obscure, which results in difficulties in understanding the mechanism of actions and side effects. To alleviate this issue, in this study, a photoaffinity probe and two fluorescent probes were created based on Crenolanib, followed by competitive protein profiling and bioimaging studies, with the aim of characterizing the cellular targets. A series of unknown protein hits, such as MAPK1, SHMT2, SLC25A11, and HIGD1A, were successfully identified by means of pull-down/LC-MS/MS; these might provide valuable clues for understanding drug action and potential toxicities. Moreover, the fluorescent probes are suitable for imaging drug distribution at the single-cell level.

Tetrazole hybrids with potential anticancer activity

Cancer is one of the main causes of death throughout the world. The anticancer agents are indispensable for the treatment of various cancers, but most of them currently on the market are not specific, resulting in series of side effects of chemotherapy. Moreover, the emergency of drug-resistance towards cancers has already increased up to alarming level in the recent decades. Therefore, it's imperative to develop novel anticancer candidates with excellent activity against both drug-susceptible and drug-resistant cancers, and low toxicity as well. Tetrazole is the bioisoster of carboxylic acid, and its derivatives demonstrated promising anticancer activity. Hybridization of tetrazole with other anticancer pharmacophores may provide novel candidates with anticancer potency. The present review described the anticancer activity of tetrazole hybrids, and the structure-activity relationship (SAR) is also discussed to provide an insight for rational designs of tetrazole anticancer candidates with higher efficiency.

Integrated phenotypic screening and activity-based protein profiling to reveal potential therapy targets of pancreatic cancer

Pancreatic cancer has been defined as one of the most complex and challenging cancers to treat, but very few valid therapeutic targets have been identified to date. To address this issue, a 61-compound library was readily created by Ugi reaction followed by phenotypic screening, leading to the discovery of two most potent inhibitors, P21 and P26, which significantly impair BxPC-3 pancreatic cancer cell survival. A series of interacting protein hits, such as GSTO1, FAM213A, RAB6A/6B/39A and USMG5, were subsequently identified by quantitative chemoproteomics studies. The main cellular target, GSTO1, was further validated as a novel pancreatic cancer therapeutic target.

Minimalist linkers suitable for irreversible inhibitors in simultaneous proteome profiling, live-cell imaging and drug screening

A series of minimalist linkers were developed and have been demonstrated to be suitable for irreversible inhibitors in simultaneous proteome profiling, live-cell imaging and drug screening, thus facilitating the discovery of first-in-class anticancer drugs.

Opportunities for Lipid-Based Probes in the Field of Immunology

Lipids perform a wide range of functions inside the cell, ranging from structural building block of membranes and energy storage to cell signaling. The mode of action of many signaling lipids has remained elusive due to their low abundance, high lipophilicity, and inherent instability. Various chemical biology approaches, such as photoaffinity or activity-based protein profiling methods, have been employed to shed light on the biological role of lipids and the lipid-protein interaction profile. In this review, we will summarize the recent developments in the field of chemical probes to study lipid biology, especially in immunology, and indicate potential avenues for future research.

Discovery of Arabidopsis UGT73C1 as a steviol-catalyzing UDP-glycosyltransferase with chemical probes

A strategy for rapidly mining biological parts from plants for synthetic biology utilizing natural product-derived chemical probes has been reported.

Tetrazole-Based Probes for Integrated Phenotypic Screening, Affinity-Based Proteome Profiling, and Sensitive Detection of a Cancer Biomarker

Target-identification phenotypic screening has been a powerful approach in drug discovery; however, it is hindered by difficulties in identifying the underlying cellular targets. To address this challenge, we have combined phenotypic screening of a fully functionalized small-molecule library with competitive affinity-based proteome profiling to map and functionally characterize the targets of screening hits. Using this approach, we identified ANXA2, PDIA3/4, FLAD1, and NOS2 as primary cellular targets of two bioactive molecules that inhibit cancer cell proliferation. We further demonstrated that a panel of probes can label and/or image annexin A2 (a cancer biomarker) from different cancer cell lines, thus providing opportunities for potential cancer diagnosis and therapy.