Streamlined Target Deconvolution Approach Utilizing a Single Photoreactive Chloroalkane Capture Tag.

Identification of physiologically relevant targets for lead compounds emerging from drug discovery screens is often the rate-limiting step toward understanding their mechanism of action and potential for undesired off-target effects. To this end, we developed a streamlined chemical proteomic approach utilizing a single, photoreactive cleavable chloroalkane capture tag, which upon attachment to bioactive compounds facilitates selective isolation of their respective cellular targets for subsequent identification by mass spectrometry. When properly positioned, the tag does not significantly affect compound potency and membrane permeability, allowing for binding interactions with the tethered compound (probe) to be established within intact cells under physiological conditions. Subsequent UV-induced covalent photo-cross-linking "freezes" the interactions between the probe and its cellular targets and prevents their dissociation upon cell lysis. Targets cross-linked to the capture tag are then efficiently enriched through covalent capture onto HaloTag coated beads and subsequent selective chemical release from the solid support. The tag's built-in capability for selective enrichment eliminates the need for ligation of a capture tag, thereby simplifying the workflow and reducing variability introduced through additional operational steps. At the same time, the capacity for adequate cross-linking without structural optimization permits modular assembly of photoreactive chloroalkane probes, which reduces the burden of customized chemistry. Using three model compounds, we demonstrate the capability of this approach to identify known and novel cellular targets, including those with low affinity and/or low abundance as well as membrane targets with several transmembrane domains.

Bisubstrate-Type Chemical Probes Identify GRP94 as a Potential Target of Cytosine-Containing Adenosine Analogs.

We synthesized affinity-based chemical probes of cytosine-adenosine bisubstrate analogs and identified several potential targets by proteomic analysis. The validation of the proteomic analysis identified the chemical probe as a specific inhibitor of glucose-regulated protein 94 (GRP94), a potential drug target for several types of cancers. Therefore, as a result of the use of bisubstrate-type chemical probes and a chemical-biology methodology, this work opens the way to the development of a new family of GRP94 inhibitors that could potentially be of therapeutic interest.

Identification of Protein Targets of Bioactive Small Molecules Using Randomly Photomodified Probes.

Identifying protein targets of bioactive small molecules often requires complex, lengthy development of affinity probes. We present a method for stochastic modification of small molecules of interest with a photoactivatable phenyldiazirine linker. The resulting isomeric mixture is conjugated to a hydrophilic copolymer decorated with biotin and a fluorophore. We validated this approach using known inhibitors of several medicinally relevant enzymes. At least a portion of the stochastic derivatives retained their binding to the target, enabling target visualization, isolation, and identification. Moreover, the mix of stochastic probes could be separated into fractions and tested for binding affinity. The structure of the active probe could be determined and the probe resynthesized to improve binding efficiency. Our approach can thus enable rapid target isolation, identification, and visualization, while providing information required for subsequent synthesis of an optimized probe.

Comparison of the photochemical behavior of four different photoactivatable probes.

The most commonly used photoaffinity labeling probes are compared, which are aryl azides, aryl diazirines, alpha-diazocarbonyls and benzophenone-derivatives. The compounds were used under identical conditions and crosslinking efficiency, influence of water, irradiation requirements, and by-products were investigated. Using the pentapeptide thymopentin (TP5) as a model system, we synthesized four analogues by solid-phase peptide synthesis and partially N-terminal modification to obtain [p-(3-trifluoromethyl)diazirinophenylalanine5]TP5, [p-benzoylphenylalanine5]TP5, 4-azidobenzoyl-TP5 and 2-diazo-3,3,3-trifluoropropionyl-TP5. The peptides were characterized by HPLC and ion-spray mass spectroscopy. Irradiation of the peptides with two different ultraviolet sources was carried out in water, n-propanol and water/n-propanol to imitate both hydrophobic and hydrophilic peptide/protein-interactions as well as the influence of the aqueous environment. Analysis of the products with HPLC, ion-spray MS, HPLC-MS and HPLC-CID-MS revealed that (Tmd)Phe is a highly potent carbene-precursor, which can be transformed easily into uniform crosslinking products by smooth photolysis. However, the electrophilic nature of the intermediate causes a high tendency to react with water molecules. The 4-azidobenzoyl group showed comparable crosslinking efficiency, but the probability to create non-uniform irradiation products (e.g. through rearrangement) is higher, whereas the reaction with water is less dominant. In contrast, Bpa was found to have an extremely low affinity to react with water, whereas prolonged UV irradiation is needed to get complete rearrangement into a variety of products. As the absorption band of alpha-diazocarbonyls at around 350 nm possesses a low extinction coefficient, 2-diazo-3,3,3-trifluoropropionyl-TP5 could not be activated at all with the optimized irradiation conditions that we have chosen for our comparative studies.

Photochemical reactions of azidocoumarins.

Photochemical reactions of 6-azidocoumarin and 7-azido-4-methylcoumarin in the presence of secondary amines have been investigated for their potential applications in photoaffinity labeling. It was found that the singlet nitrene generated from 6-azidocoumarin isomerized to a dehydroazepine intermediate that reacted with an amine to yield two isomeric adducts. Photolysis of 7-azido-4-methylcoumarin, in contrast, gave a triplet nitrene that abstracted hydrogen atoms from secondary amine molecules to form 7-amino-4-methylcoumarin as the major product. The difference in the intersystem crossing rate between the two compounds originates from the azido position relative to the carbonyl group. Because of its ability to form a covalent linkage with a nucleophile, 6-azidocoumarin is deemed to have a greater potential as a photoaffinity label than 7-azido-4-methylcoumarin.

Photoaffinity cross-linking of TaqI restriction endonuclease using an aryl azide linked to the phosphate backbone.

In an effort to identify amino acid (aa) residues near the active site of TaqI restriction endonuclease (ENase), a sequence-specific photoaffinity reagent was designed. This reagent exploits the finding that modification of the Rp oxygen of the scissile phosphate does not interfere with substrate binding. The TpCGA phosphate was substituted with an Rp phosphorothioate group to direct the placement of the heterobifunctional reagent p-azidophenacyl bromide. TaqI bound the photoaffinity reagent specifically and formed a covalent adduct with the ENase in the presence of UV light. The modified aa was identified as Tyr161. This aa was changed to Phe by site-directed mutagenesis, and the resulting Y161F mutant was characterized. Removal of the Tyr161 hydroxyl group lowered both the kcat and the Km fivefold, indicating that, while this aa may be near the scissile phosphate, it is not critically required for catalysis.

Acceptor helix interactions in a class II tRNA synthetase: photoaffinity cross-linking of an RNA miniduplex substrate.

The 875 amino acid class II Escherichia coli alanine tRNA synthetase aminoacylates hairpin minihelices and miniduplexes comprising complementary base pairs that reconstruct the acceptor helix of alanine tRNA. Aminoacylation is dependent upon a G3:U70 base pair in the tRNA acceptor stem. A synthetic RNA miniduplex with a phosphorothioate internucleotide linkage on the 5'-side of U70 facilitated the stable attachment of a pendant benzophenone to the ribonucleotide backbone. The benzophenone-labeled duplex is active for aminoacylation. Irradiation of the labeled duplex produced a cross-linked RNA protein complex, in which the major site of RNA attachment is the segment between the class II defining sequence motifs 2 and 3. This segment spans a putative zinc-binding motif, which has been implicated in acceptor helix recognition, and is within a 461 amino acid N-terminal fragment that was recently shown to have full activity for minihelix aminoacylation. These results, together with the X-ray crystallographic investigations of the class II aspartate tRNA synthetase-tRNA(Asp) complex, suggest that the segment between motifs 2 and 3 in the 10 class II synthetases contributes generally to the docking of tRNA acceptor helices. The sequence diversity of this segment implies that its mode of interaction with the acceptor helix is idiosyncratic to the class II enzyme.

Active site labeling of HIV-1 reverse transcriptase.

The human immunodeficiency virus-1 reverse transcriptase (HIV-1 RT) heterodimer (M(r) = 66,000 and M(r) = 51,000) has been photoaffinity labeled using 4-thiodeoxyuridine triphosphate (S4-dUTP) as a probe. A nascent polymerization complex was assembled from a single-stranded DNA template, a 12-mer DNA primer, and the necessary dNTPs (one of which was alpha-32P-labeled) to extend the primer to produce the n-1 product. The photoaffinity probe was then uniquely added at the 3'-terminal position of the extended primer bound at the catalytic site and photolyzed. The larger subunit (p66) was exclusively derivatized. The unique radioactive peptide resulting from proteolysis was isolated and identified by amino acid sequencing.

Photoaffinity labeling of an acorn barnacle lectin with a photoactivatable fluorescent reagent derivative of D-galactosamine.

A photoactivatable D-galactosamine derivative was prepared by reaction of the amino group of D-galactosamine with 1-azide-5-naphthalene sulfonyl chloride (ANS-Cl). The derivative (GalN-ANS) inhibited the agglutination activity of an acorn barnacle lectin against rabbit erythrocytes to the same extent as D-galactosamine. We used GalN-ANS for photoaffinity labeling of the lectin. The photolabeled lectin was digested with pronase and the digest was separated by reversed-phase high-performance liquid chromatography by monitoring fluorescence and uv absorption to isolate the peptide labeled with GalN-ANS. Amino acid analyses of the labeled peptides revealed that GalN-ANS preferentially covalently labeled two regions in the carbohydrate recognition domain of the lectin. One of them was the highly conserved amino-acid sequence region throughout all calcium-dependent animal lectins.

Photoaffinity labeling of the angiotensin II receptor. 3. Receptor inactivation with photolabile hormone analogues.

It has been shown that the receptor of angiotensin II (AT) in rabbit aorta strips, rat aorta, and rat stomach can be blocked specifically and irreversibly by several photolabile analogues of Sar-Arg-Val-Tyr-Val-His-Pro-Phe ([Sar1]AT) with irradiation. The effectiveness of a photolabel with light of wavelength 365 nm depends on the labeling amino acid (L-4'-nitrophenylalanine, L-4'-diazoniumphenylalanine, or L-4'-azidophenylalanine) and on its position in the peptide (replacing Tyr4 and/or Phe8). The 4'-azido)Phe-containing analogues are all good to fair photoinactivators. Their decreasing order of effectiveness is as follows: [Sar1,(4'-azido)Phe8]AT, [Sar1,(4'-azido)Phe4,8]AT, and [Sar1,(4'-azidoPhe4]AT. The (4'-nitro)Phe analogues show the opposite relation: the good ligand [Sar1,(4'-nitro)Phe8]AT is almost ineffective, but the nonligand [Sar1,(4-nitro)Phe4]AT exhibits good, specific photoinactivation. This can be explained by the existence of a different photolysis pathway for (4'-nitro)Phe: this analogue probably undergoes a multiphoton decay with a long-lived first excited state. A peptide in this state may differ in its pharmacological properties from the ground state and become a ligand.