Phosphorus-Based Probes as Molecular Tools for Proteome Studies: Recent Advances in Probe Development and Applications

Abstract

Studies on the human proteome have engaged diverse techniques; however, none of them represent a predominant approach. Chemical biology has made a major contribution to our understanding of human biology, stimulating the generation of biological hypotheses. Tools such as functional probes have advanced studies on biological mechanisms and helped in elucidating off-target reactivity and potential toxicities of drugs and drug candidates. Here, we accentuate the recent developments in the design and applications of phosph(on)ate-containing probes. Phosphate esters and anhydrides are present in a number of vital cell constituents, and their significance can be reflected by a number of biological processes that involve phosphorus-bearing molecules. We discuss the use of phosph(on)ate-derived probes for (1) the identification of phosphate-requiring enzymes, their substrates, interacting partners; (2) developing screening assays; and (3) their potential as diagnostics. Limitations that as yet need to be overcome and possible measures to be undertaken will also be addressed.

Chemical proteomic profiling reveals protein interactors of the alarmones diadenosine triphosphate and tetraphosphate

“…The used DA represents a small functional group that undergoes carbene formation under UV light that rapidly inserts into nearby C–H, N–H, and O–H bonds, rendering DAs well-established tools for photoaffinity labeling 19 , 20 . DTB as affinity tag allows enrichment of tagged proteins by exploiting the affinity of DTB to (strept)avidin, and its specific elution with biotin for subsequent analysis by high-resolution mass spectrometry (MS) 21 , 22 . The synthesis of both probes was straightforward and is described in detail in Supplementary Figs.…”

Covalent Small Molecules as Enabling Platforms for Drug Discovery

“…This reaction transfers a biotin tag onto the protein, which can then be used as an enrichment handle for downstream MS analysis . By competing the binding of these probes with small molecules, assessment of target engagement and kinome‐wide selectivity in cell lysates can be achieved . Although this technology represents a major technological progression, one of the key limitations of the KiNativ platform is that these probes are not cell‐permeable.…”

Development of Fluorophosphoramidate as a Biocompatibly Transformable Functional Group and its Application as a Phosphate Prodrug for Nucleoside Analogs

“…[8] Several enzymes are involved in the conversion and recognition of a phosphate group. Thus, many types of phosphate-based synthetic functional groups that can work as designed in vivo have been developed and applied to bioprobes [9][10][11][12] and drugs. [13][14][15] In this context, development of a new type of biocompatible phosphate-based functional group would be beneficial both in chemical biology and medicinal chemistry.…”