Kaori Sakurai

Reaction discovery enabled by DNA-templated synthesis and in vitro selection

Current approaches to reaction discovery focus on one particular transformation. Typically, researchers choose substrates based on their predicted ability to serve as precursors for the target structure, then evaluate reaction conditions for their ability to effect product formation. This approach is ideal for addressing specific reactivity problems, but its focused nature might leave many areas of chemical reactivity unexplored. Here we report a reaction discovery approach that uses DNA-templated organic synthesis and in vitro selection to simultaneously evaluate many combinations of different substrates for bond-forming reactions in a single solution. Watson–Crick base pairing controls the effective molarities of substrates tethered to DNA strands; bond-forming substrate combinations are then revealed using in vitro selection for bond formation, PCR amplification and DNA microarray analysis. Using this approach, we discovered an efficient and mild carbon–carbon bond-forming reaction that generates an enone from an alkyne and alkene using an inorganic palladium catalyst. Although this approach is restricted to conditions and catalysts that are at least partially compatible with DNA, we expect that its versatility and efficiency will enable the discovery of additional reactions between a wide range of substrates.

In Vitro Selection of a DNA-Templated Small-Molecule Library Reveals a Class of Macrocyclic Kinase Inhibitors

DNA-templated organic synthesis enables the translation of DNA sequences into synthetic small-molecule libraries suitable for in vitro selection. Previously, we described the DNA-templated multistep synthesis of a 13 824-membered small-molecule macrocycle library. Here, we report the discovery of small molecules that modulate the activity of kinase enzymes through the in vitro selection of this DNA-templated small-molecule macrocycle library against 36 biomedically relevant protein targets. DNA encoding selection survivors was amplified by PCR and identified by ultra-high-throughput DNA sequencing. Macrocycles corresponding to DNA sequences enriched upon selection against several protein kinases were synthesized on a multimilligram scale. In vitro assays revealed that these macrocycles inhibit (or activate) the kinases against which they were selected with IC50 values as low as 680 nM. We characterized in depth a family of macrocycles enriched upon selection against Src kinase, and showed that inhibition was highly dependent on the identity of macrocycle building blocks as well as on backbone conformation. Two macrocycles in this family exhibited unusually strong Src inhibition selectivity even among kinases closely related to Src. One macrocycle was found to activate, rather than inhibit, its target kinase, VEGFR2. Taken together, these results establish the use of DNA-templated synthesis and in vitro selection to discover small molecules that modulate enzyme activities, and also reveal a new scaffold for selective ATP-competitive kinase inhibition.

Comparison of the Reactivity of Carbohydrate Photoaffinity Probes with Different Photoreactive Groups

A judicious choice of photoreactive group is critical in successful photoaffinity labeling studies of small molecule–protein interactions. A set of carbohydrate‐based photoaffinity probes was prepared to compare the effects of three major photoreactive groups on the efficiency and selectivity of crosslinking a binding protein with low affinity. We showed that, despite the low crosslinking yield, the diazirine probe displayed the high ligand‐dependent reactivity consistent with the ideal mechanism of photoaffinity labeling. Moreover, we demonstrated that, among the three photoreactive groups, only the diazirine probe achieved highly selective crosslinking of a low‐affinity binding protein in cell lysate.

Active/Inactive Dual-Probe System for Selective Photoaffinity Labeling of Small Molecule-Binding Proteins

Two are better than one: A new approach to selective photoaffinity labeling is described in which a bioactive probe is used in combination with its inactive analog as a scavenger of nonspecific proteins.

Three-dimensional structures of OSW-1 and its congener.

The 3D structures of an antitumor glycosylsterol OSW-1 and its closely related congener were investigated by NMR studies and an X-ray crystallographic analysis. The disaccharide moiety was found as a structural scaffold for the formation of a hydrophobic cluster by the biologically required functionalities.

Selective fluorescence detection of small-molecule-binding proteins by using a dual photoaffinity labeling system.

PHOTO OPPORTUNITY: We have developed a dual photoaffinity labeling system in which an active and an inactive probe bearing orthogonal detection groups are co-reacted in a single photoreaction. The approach allowed selective fluorescent detection of a model binding protein in cell lysate by either 1D or 2D electrophoresis.

Synthesis of OSW-1 derivatives by site-selective acylation and their biological evaluation.

A strategy to site-selectively monoacylate an antitumor saponin OSW-1 was developed using an organotin reagent to rapidly access its derivatives that are useful as chemical probes. 4″-O-Acylated OSW-1 derivatives bearing a fluorophore, an alkyne tag, or biotin were prepared in good yields and were shown to maintain highly cytotoxic activity.

Photoaffinity labeling studies of the carbohydrate-binding proteins with different affinities

Photoaffinity labeling has been used as a promising approach to detection and isolation of carbohydrate-binding proteins, which are typically characterized by low binding affinity and selectivity. When there are several specific binding proteins, it is desirable that a photoaffinity probe is capable of simultaneously crosslinking them and that the crosslinking yields depend on the relative binding affinities. In this study, we describe the design and synthesis of carbohydrate photoaffinity probes and their ability to capture lectins of different binding affinities.

Fluorescent analog of OSW-1 and its cellular localization

OSW-1 is a steroidal saponin, which has emerged as an attractive anticancer agent with highly cancer cell selective activity. A fluorescent analog was prepared from the natural product to analyze its cellular uptake and localization. We found that the fluorescent analog is rapidly internalized into cells and is primarily distributed in endoplasmic reticulum and Golgi apparatus.

Design and synthesis of fluorescent glycolipid photoaffinity probes and their photoreactivity

Glycolipid-protein interactions at the cell surface are implicated in various biological processes. Toward the investigation of glycolipid binding proteins, we designed and synthesized trifunctional photoaffinity probes, which present a sugar head group with a triazole linkage to the lipid tail unit containing a photoreactive group and a fluorescent tag. The glycolipid photoaffinity probes bearing benzophenone group or diazirine group were evaluated for their photocrosslinking reactivity toward a carbohydrate head group specific protein. The diazirine based glycolipid photoaffinity probe was found to be more effective than the benzophenone-based probe in a comparative analysis involving a competitive ligand to distinguish a specific binding protein.