Activity-based proteomic profiling: application of releasable linker in photoaffinity probes

Synthetic Approaches of Epoxysuccinate Chemical Probes

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.

Discovery of Imaging and Therapeutic Integration Bifunctional Molecules Based on Bio-Orthogonal Reaction and Releasable Disulfide Bond

The application of conventional fluorescent probes in living cells has been limited by excess fluorescence interference, reduced selectivity, and poor permeability. Herein, we describe a convenient solution for overcoming the above limitations based on bio-orthogonal reactions and releasable linkers that provide bifunctional molecules for imaging and therapeutic integration. To reduce the interference of excess fluorescent moieties, a bio-orthogonal reaction was applied to activate the fluorescence of the active parent drugs without fluorophores. Moreover, disulfide bonds were incorporated as releasable linkers. After imaging the target protein, the newly yielded fluorophore could be released from the active drugs based on the highly reducing conditions of the tumor. Thus, these bifunctional molecules are comparable in therapeutic activity to the parent drug. These novel imaging and therapeutic integration molecules could be used to realize imaging-aided diagnosis and perform efficient real-time monitoring of cancer cells. Our findings are expected to enable efficient and specific imaging and real-time in vivo prognostic monitoring in the clinic.

Tumor-microenvironmental-response Bi-functional molecules for efficient imaging and anti-tumor activity therapy

To improve the visualization and potency of anticancer agents, the diagnosis and treatment integration bi-functional molecules were constructed based on active candidate BD7, approved drug Linifanib, and monoclonal antibody Bevacizumab. Commercial available Rhodamine B was inducted to realize imaging-aided diagnosis and target efficiency monitoring for cancer cells. In order to maintain the anticancer activity of drugs, disulfide bond was incorporated as releasable group based on tumor microenviroment. After design, synthesis and structure characterization of title compounds, various biological evaluation and cancer cell imaging analysis were carried out. The results indicated that these title diagnosis and treatment integration bi-functional molecules exhibited comparable potency with that of corresponding parent drug. Meanwhile, these agents afforded good performance in cell imaging and could be used to differentiate cancer cells from normal ovarian cells in real time. Further optimization of these bi-functional molecules is ongoing to improve the potency and precision and will be reported in due course. Our findings are expected to achieve efficient screening and real-time prognostic monitoring under the premise of high anti-tumor activity for clinical application.

Selectivity aspects of activity-based (chemical) probes

Selective chemical modulators are ideal tools to study the function of a protein. Yet, the poor ligandability of many proteins has hampered the development of specific chemical probes for numerous protein classes. Tools, such as covalent inhibitors and activity-based protein profiling, have enhanced our understanding of thus-far difficult-to-target proteins and have enabled correct assessment of the selectivity of small-molecule modulators. This also requires deeper knowledge of compound and target site reactivity, evaluation of binding to noncovalent targets and protein turnover. The availability of highly selective chemical probes, the evolution of activity-based probes, and the development of profiling methods will open a new era of drugging the undruggable proteome.

Research Progress and Application of Bioorthogonal Reactions in Biomolecular Analysis and Disease Diagnosis

Bioorthogonal reactions are rapid, specific and high yield reactions that can be performed in in vivo microenvironments or simulated microenvironments. At present, the main biorthogonal reactions include Staudinger ligation, copper-catalyzed azide alkyne cycloaddition, strain-promoted [3 + 2] reaction, tetrazine ligation, metal-catalyzed coupling reaction and photo-induced biorthogonal reactions. To date, many reviews have reported that bioorthogonal reactions have been used widely as a powerful tool in the field of life sciences, such as in target recognition, drug discovery, drug activation, omics research, visualization of life processes or exogenous bacterial infection processes, signal transduction pathway research, chemical reaction dynamics analysis, disease diagnosis and treatment. In contrast, to date, few studies have investigated the application of bioorthogonal reactions in the analysis of biomacromolecules in vivo. Therefore, the application of bioorthogonal reactions in the analysis of proteins, nucleic acids, metabolites, enzyme activities and other endogenous molecules, and the determination of disease-related targets is reviewed. In addition, this review discusses the future development opportunities and challenges of biorthogonal reactions. This review presents an overview of recent advances for application in biomolecular analysis and disease diagnosis, with a focus on proteins, metabolites and RNA detection.

Effective and transient mapping of protein-protein interactions: Application of novel releasable photoaffinity linkers

Herein, two novel multifunctional releasable photoaffinity linkers were developed for effective and transient tracking interacting proteins with the overall objective of understanding their in vivo biological functions in real-time. These linkers could be used for the chemical modification of protein under moderate experimental conditions to form protein photoaffinity probes. These probes incorporated with both photoaffinity labels and tag-transfer, enable photo-crosslinking of bait proteins along with the release of unrelated groups. These photoaffinity linkers can be utilized to construct probes for disease markers, which could enable rapid diagnosis in a clinical setting at minimal interference with normal physiology.

Exploring the potential intracellular targets of vascular normalization based on active candidates

We previously developed two candidates with potency of inducing vascular normalization, BD7 and B14. However, the definite intracellular molecular target(s) responsible for their activity remains unknown. Herein, we report the discovery and functional assessment of several multifunctional photoaffinity probes for determining the potential biological targets of active compounds. The probes bear a photoaffinity moiety and a bioorthogonal unit attached to B7 or B14 and maintained the bioactivity of the parent active molecules. Using in vitro biological assays, we preliminarily identified VEGFR-2 as a potential intracellular target for the active candidates. Our results demonstrate the utility of these multifunctional photoaffinity probes for analyzing the biological activity and subcellular localization of the intracellular target proteins of active candidates.

Detectives and helpers: Natural products as resources for chemical probes and compound libraries

About 70% of the drugs in use are derived from natural products, either used directly or in chemically modified form. Among all possible small molecules (not greater than 5 kDa), only a few of them are biologically active. Natural product libraries may have a higher rate of finding "hits" than synthetic libraries, even with the use of fewer compounds. This is due to the complementarity between the "chemical space" of small molecules and biological macromolecules such as proteins, DNA and RNA, in addition to the three-dimensional complexity of NPs. Chemical probes are molecules which aid in the elucidation of the biological mechanisms behind the action of drugs or drug-like molecules by binding with macromolecular/cellular interaction partners. Probe development and application have been spurred by advancements in photoaffinity label synthesis, affinity chromatography, activity based protein profiling (ABPP) and instrumental methods such as cellular thermal shift assay (CETSA) and advanced/hyphenated mass spectrometry (MS) techniques, as well as genome sequencing and bioengineering technologies. In this review, we restrict ourselves to a survey of natural products (including peptides/mini-proteins and excluding antibodies), which have been applied largely in the last 5 years for the target identification of drugs/drug-like molecules used in research on infectious diseases, and the description of their mechanisms of action.

Bifunctional Non-Canonical Amino Acids: Combining Photo-Crosslinking with Click Chemistry

Genetic code expansion is a powerful tool for the study of protein interactions, as it allows for the site-specific incorporation of a photoreactive group via non-canonical amino acids. Recently, several groups have published bifunctional amino acids that carry a handle for click chemistry in addition to the photo-crosslinker. This allows for the specific labeling of crosslinked proteins and therefore the pulldown of peptides for further analysis. This review describes the properties and advantages of different bifunctional amino acids, and gives an overview about current and future applications.