Click Chemistry is a powerful tool to probe for the cellular localization of small molecules. Knowing where a small molecules goes in the cell gives powerful insights into their mechanisms of action. This approach has been used in numerous studies, and discoveries include that salinomycin localizes to lysosomes to initiate ferroptosis in cancer stem cells and that metformin derivatives accumulate in mitochondria to chelate copper(II), affecting metabolism and epigenetic changes downstream in inflammatory macrophages.
The commercial potential of click chemistry is great. The fluorophore rhodamine has been coupled onto norbornene, and reacted with tetrazine in living systems. In other cases, SPAAC between a cyclooctyne-modified fluorophore and azide-tagged proteins allowed the selection of these proteins in cell lysates.
Methods for the incorporation of click reaction partners into systems in and ex vivo contribute to the scope of possible reactions. The development of unnatural amino acid incorporation by ribosomes has allowed for the incorporation of click reaction partners as unnatural side groups on these unnatural amino acids. For example, an UAA with an azide side group provides convenient access for cycloalkynes to proteins tagged with this "AHA" unnatural amino acid. In another example, "CpK" has a side group including a cyclopropane alpha to an amide bond that serves as a reaction partner to tetrazine in an inverse diels-alder reaction.
The synthesis of luciferin exemplifies another strategy of isolating reaction partners, which is to take advantage of rarely-occurring, natural groups such as the 1,2-aminothiol, which appears only when a cysteine is the final N amino acid in a protein. Their natural selectivity and relative bioorthogonality is thus valuable in developing probes specific for these tags. The above reaction occurs between a 1,2-aminothiol and a 2-cyanobenzothiazole to make luciferin, which is fluorescent. This luciferin fluorescence can be then quantified by spectrometry following a wash, and used to determine the relative presence of the molecule bearing the 1,2-aminothiol. If the quantification of non-1,2-aminothiol-bearing protein is desired, the protein of interest can be cleaved to yield a fragment with a N Cys that is vulnerable to the 2-CBT.
Additional applications include:
*two-dimensional gel electrophoresis separation
*preparative organic synthesis of 1,4-substituted triazoles
*modification of peptide function with triazoles
*modification of natural products and pharmaceuticals
*natural product discovery 
*drug discovery
*macrocyclizations using Cu(I) catalyzed triazole couplings
*modification of DNA and nucleotides by triazole ligation
*supramolecular chemistry: calixarenes, rotaxanes, and catenanes
*dendrimer design
*carbohydrate clusters and carbohydrate conjugation by Cu(1) catalyzed triazole ligation reactions
*polymers and biopolymers
*surfaces
*material science
*nanotechnology,
* bioconjugation, for example, azidocoumarin, and 
*biomaterials
In combination with combinatorial chemistry, high-throughput screening, and building chemical libraries, click chemistry has hastened new drug discoveries by making each reaction in a multistep synthesis fast, efficient, and predictable.