The Skaggs Institute
for Chemical Biology

Scientific Report 2006

Click Chemistry: Diversity and Function From a Few Reactions

K.B. Sharpless, V.V. Fokin, M. Ahlquist, B. Boren, M. Cassidy, S. Chang, A. Feldman, J. Fotsing, R. Fraser, A. Grant, J. Hein, J. Kalisiak, L. Krasnova, S.-W. Kwok, Y. Liu, J. Loren, R. Manetsch, K. Nagai, S. Narayan, S. Pitram, L.K. Rasmussen, J. Raushel, S. Roeper, W. Sharpless, A. Sugawara, J. Tripp, X. Wang, J. Wassenaar, T. Weide, M. Whiting, P. Wu

During the past decade, the laborious process of discovering and optimizing compounds that may be useful as drugs has been aided by combinatorial chemistry, which allows generation of large collections of test compounds for screening. However, in order to produce useful chemically diverse libraries of compounds, individual reactions involved in combinatorial syntheses must be supremely reliable. Click chemistry is an approach to synthesis that we have developed during the past 5 years. Our goal is to facilitate the discovery process through the use of a few nearly perfect chemical reactions for the synthesis and assembly of specially designed building blocks. These building blocks have a high built-in energy content that drives a spontaneous, selective, and irreversible linkage reaction with complementary sites in other blocks.

In click chemistry, searches for function are restricted to molecules that are easy to make. For the discovery of possibly useful compounds, this strategy provides a means for the rapid exploration of the chemical space. For optimization of compounds, the method enables rapid structure-activity profiling through generation of analog libraries. Click chemistry–based searches are fast, because they avoid the regions of the chemical universe that are difficult to access. They are wide-ranging, because of the use of strongly driven, highly selective reactions of broad scope, allowing the use of a much greater diversity of building blocks. Click chemistry does not replace existing methods for drug discovery, rather it complements and extends them. It works well in conjunction with structure-based design and combinatorial chemistry techniques and, through the choice of appropriate building blocks, can provide derivatives or mimics of “traditional” pharmacophores, drugs, and natural products. However, the real power of click chemistry is the ability to generate novel structures that might not necessarily resemble known biologically active compounds.

Click chemistry is both enabled and constrained by reliance on a few nearly perfect reactions, and this characteristic raises concerns about limitations on the access of click chemistry to chemical diversity. A computational study suggests that the pool of “druglike” compounds is as large as 10⁶³. Currently, only a few million compounds that fulfill these criteria are known, implying that only an infinitesimal part of the potential medicinal chemistry universe has been explored so far. These facts have staggering implications for drug discovery. First and foremost, most molecules with useful properties remain to be discovered. Second, the majority of useful new compounds most likely will be found in unconventional structure space. Thus, with click chemistry, we have the interesting proposition that greater diversity can be achieved with fewer reactions, because it is not the number of reactions that is important, but the reach of the reactions, which is determined by the tolerance to variations in the nature of their components. Click chemistry approaches have already proved themselves in biomedical research, ranging from combinatorial chemistry to bioconjugation strategies in proteomics; in polymer chemistry; and in materials science.

Inhibitors of HIV Type 1 Protease Via in Situ Click Chemistry

Although click chemistry is a powerful way to rapidly assemble diverse collections of molecules, further evolution of the molecules is traditionally achieved by iterative cycles of screening for biological activity and synthetic modification. Can direct involvement of the target, usually a specific receptor or enzyme, in the selection and evolution of possible drug candidates accelerate this drug discovery cycle? The aim of in situ click chemistry is to accelerate the discovery cycle by engaging an enzyme in the selection and covalent assembly of its own “best fitting” inhibitor. Although the concept has been previously tested by several researchers, in situ click chemistry is unique because it relies on the completely bioorthogonal 1,3-dipolar cycloaddition of organic azides and alkynes. This highly exergonic reaction produces 5-membered nitrogen heterocycles, 1,2,3-triazoles, which are exceedingly stable to acidic and basic hydrolysis and to severe reduction-oxidation conditions. At the same time, the triazoles produced can actively participate in hydrogen-bonding, dipole-dipole, and p-stacking interactions.

Even though both azides and alkynes are energetic species, their reactivity profiles are quite narrow, at least under physiologic conditions. Furthermore, despite the large thermodynamic driving force for cycloaddition, the high kinetic barrier effectively hides the reactants until they are brought into proximity by a biological template. These features allow the target to sample numerous combinations of building blocks but synthesize only the best binders.

The efficacy of in situ click chemistry has already been demonstrated by the discovery of novel, highly potent inhibitors of acetylcholinesterase and carbonic anhydrase. However, in these studies, researchers used building blocks with high affinity for the target. Not having such luxury in our attempts to produce inhibitors of HIV type 1 protease, we were pleased to find that the enzyme selectively formed an inhibitor from components that had only weak binding to the target (Fig. 1) when mixtures of azide- and alkyne-containing fragments were incubated with the protease for 24–48 hours. Encouraged by these results, we are continuing our collaboration with J.H. Elder and A.J. Olson, Scripps Research, to rapidly identify potent inhibitors of HIV protease mutants.

Fig. 1. Formation of an HIV type 1 protease inhibitor.

Publications

Bourne, Y., Radic, Z., Kolb, H.C., Sharpless, K.B., Taylor, P., Marchot, P. Structural insights into conformational flexibility at the peripheral site and within the active center gorge of AchE. Chem. Biol. Interact. 157-158:159, 2005.

Cassidy, M.P., Raushel, J., Fokin, V.V. Practical synthesis of amides from in situ generated copper(I) acetylides and sulfonyl azides. Angew. Chem. Int. Ed. 45:3154, 2006.

Dìaz, D.D., Converso, A., Sharpless, K.B., Finn, M.G. 2,6-Dichloro-9-thiabicyclo-[3.3.1]nonane: multigram display of azide and cyanide components on a versatile scaffold. Molecules 11:212, 2006.

Hansen, T.V., Wu, P., Fokin, V.V. One-pot copper(I)-catalyzed synthesis of 3,5-disubstituted isoxazoles. J. Org. Chem. 70:7761, 2005.

Malkoch, M., Schleicher, K., Drockenmuller, E., Hawker, C.J., Russell, T.P., Wu, P., Fokin, V.V. Structurally diverse dendritic libraries: a highly efficient functionalization approach using click chemistry. Macromolecules 38:3663, 2005.

Meng, J.-C., Fokin, V.V., Finn, M.G. Kinetic resolution by copper-catalyzed azide-alkyne cycloaddition. Tetrahedron Lett. 46:4543, 2005.

Narayan, S., Fokin, V.V., Sharpless, K.B. Organic synthesis in aqueous suspension: chemistry “on water.” In: Organic Reactions in Water. Lindström, U.M. (Ed.). Blackwell, Malden, MA, in press.

Petasis, N.A., Akritopoulou-Zanze, I., Fokin, V.V., Bernasconi, G., Keledjian, R., Yang, R., Uddin, J., Nagulapalli, K.C., Serhan, C.N. Design, synthesis and bioactions of novel stable mimetics of lipoxins and aspirin-triggered lipoxins. Prostaglandins Leukot. Essent. Fatty Acids 73:301, 2005.

Radic, Z., Manetsch, R., Krasinski, A., Raushel, J., Yamauchi, J., Garcia, C., Kolb, H.C., Sharpless, K.B., Taylor, P. Molecular basis of interactions of cholinesterases with tight binding inhibitors. Chem. Biol. Interact. 157-158:133, 2005.

Rodionov, V.O., Fokin, V.V., Finn, M.G. Mechanism of the ligand-free Cu(I)-catalyzed azide-alkyne cycloaddition reaction. Angew. Chem. Int. Ed. 44:2210, 2005.

Whiting, M., Fokin, V.V. Copper-catalyzed reaction cascade: direct conversion of alkynes to N-sulfonyl azetidin-2-imines. Angew. Chem. Int. Ed. 45:3157, 2006.

Whiting, M., Muldoon, J., Lin, Y.-C., Silverman, S.M., Lindstrom, W., Olson, A.J., Kolb, H.C., Finn, M.G., Sharpless, K.B., Elder, J.H., Fokin, V.V. Inhibitors of HIV-1 protease by using in situ click chemistry. Angew. Chem. Int. Ed. 45:1435, 2006.

Whiting, M., Tripp, J., Lin, Y.-C., Lindstrom, W., Olson, A.J., Elder, J.H., Sharpless, K.B., Fokin, V.V. Rapid discovery and structure-activity profiling of novel inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(I)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization. J. Med. Chem. 49:7697, 2006.

Wu, P., Hilgraf, R., Fokin, V.V. Osmium-catalyzed olefin dihydroxylation and aminohydroxylation in the second catalytic cycle. Adv. Synth. Catal. 348:1079, 2006.

Wu, P., Malkoch, M., Hunt, J., Vestberg, R., Kaltgrad, E., Finn, M.G., Fokin, V.V., Sharpless, K.B., Hawker, C.J. Multivalent, bifunctional dendrimers prepared by click chemistry. Chem. Commun. (Camb.) 5775, 2005, Issue 46.