Synthesis and application of cleavable photoactivable heterobifunctional reagents

Affinity-based profiling of dehydrogenase subproteomes

The high cost of drug discovery and development requires more efficient approaches to the identification and inhibition of tractable protein targets. One strategy is to pursue families of proteins that already possess affinity for a drug lead scaffold, where that scaffold plays the dual role of serving (a) when tethered to a resin, as a ligand to purify a subproteome of interest, and (b) as a lead molecule that has the potential for optimization for a given member of the subproteome. Here, we describe an example of the purification of a subproteome using a scaffold tailored to the dehydrogenase family of enzymes. Combined with modern LC-MS/MS methods and subsequent searching of proteome databases, such affinity chromatography strategies can be used to purify and identify any proteins with affinity for the scaffold molecule. The method is exemplified using the CRAA (catechol rhodanine acetic acid) privileged scaffold, which is tailored to dehydrogenases. CRAA affinity column chromatography, combined with LC-MS/MS, is described as a method for profiling dehydrogenase subproteomes.

Cleavable linker for photo-cross-linked small-molecule affinity matrix

The introduction of a cleavable site in a photoactivatable linker, which is used to immobilize small molecules on an affinity matrix via a site-nonselective carbene addition/insertion reaction, makes it possible to verify the presence of the immobilized small molecule on the affinity matrix. It also permits the efficient detection of proteins covalently bound to the immobilized small molecule.

Chemical proteomics-based drug design: target and antitarget fishing with a catechol-rhodanine privileged scaffold for NAD(P)(H) binding proteins

Drugs typically exert their desired and undesired biological effects by virtue of binding interactions with protein target(s) and antitarget(s), respectively. Strategies are therefore needed to efficiently manipulate and monitor cross-target binding profiles (e.g., imatinib and isoniazid) as an integrated part of the drug design process. Herein we present such a strategy, which reverses the target --> lead rational drug design paradigm. Enabling this approach is a catechol-rhodanine privileged scaffold for dehydrogenases, which is easily tuned for affinity and specificity toward desired targets. This scaffold crosses bacterial (E. coli) cell walls, and proteome-wide studies demonstrate it does indeed bind to and identify NAD(P)(H)-binding proteins that are potential drug targets in Mycobacterium tuberculosis and antitargets (or targets) in human liver. This approach to drug discovery addresses key difficulties earlier in the process by only pursuing targets for which a chemical lead and optimization strategy are available, to permit rapid tuning of target/antitarget binding profiles.

Photoactivable analogs for labeling 25-hydroxyvitamin D3 serum binding protein and for 1,25-dihydroxyvitamin D3 intestinal receptor protein

3-Azidobenzoates and 3-azidonitrobenzoates of 25-hydroxyvitamin D3 as well as 3-deoxy-3-azido-25-hydroxyvitamin D3 and 3-deoxy-3-azido-1,25-dihydroxyvitamin D3 were prepared as photoaffinity labels for vitamin D serum binding protein and 1,25-dihydroxyvitamin D3 intestinal receptor protein. The compounds prepared were easily activated by short- or long-wavelength uv light, as monitored by uv and ir spectrometry. The efficacy of the compounds to compete with 25-hydroxyvitamin D3 or 1,25-dihydroxyvitamin D3 for the binding site of serum binding protein and receptor, respectively, was studied to evaluate the vitamin D label with the highest affinity for the protein. The presence of an azidobenzoate or azidonitrobenzoate substituent at the C-3 position of 25-OH-D3 significantly decreased (10(4)- to 10(6)-fold) the binding activity. However, the labels containing the azido substituent attached directly to the vitamin D skeleton at the C-3 position showed a high affinity, only 20- to 150-fold lower than that of the parent compounds with their respective proteins. Therefore, 3-deoxy-3-azidovitamins present potential ligands for photolabeling of vitamin D proteins and for studying the structures of the protein active sites.

Analysis of protein aggregates by combination of cross-linking reactions and chromatographic separations

Chemical cross-linking provides a method that covalently bridges near-neighbour associations within proteins and protein aggregates. Combined with chromatographic separations and protein-chemical methods, it may be used to localize and to investigate three-dimensional relations as present under natural conditions. This paper reviews the chemistry and application of cross-linking reagents and the development of combination experimental approaches in view of chromatographic separations and cross-linking reactions. Investigations of homooligomeric and heterooligomeric protein associations as well as conformational analysis are presented.

Light–Dependent, Covalent Immobilization of Biomolecules on ‘Inert’ Surfaces

We describe a novel, versatile procedure for the light-dependent immobilization of ligands to 'inert' material surfaces. Covalent immobilization of ligands differing in chemical nature and complexity is accomplished under mild and non-destructive conditions. Topical interaction of ligands with organic or inorganic surfaces is mediated by photoactivable polymers with carbene generating trifluoromethyl-aryl-diazirines which serve as linker molecules. Light activation of aryl-diazirino functions at 350 nm yields highly reactive carbenes, and covalent coupling is achieved by simultaneous carbene insertion into both the ligand and inert surface. Thus, reactive functional groups are not required on either the ligand or the supporting material. These procedures are applicable whenever ligands, from molecules to cells--synthetically or genetically produced, or isolated from biological sources--need to be immobilized for improved performance.

Synthesis of photoreactive poly(ethylene glycol) and its application to the prevention of surface-induced platelet activation

Photoreactive poly(ethylene glycol) (PEG) was synthesized by reacting 4-fluoro-3-nitrophenyl azide (FNPA) with sodium salt of PEG. The synthesized 4-azido-2-nitrophenyl PEG (ANP-PEG) was characterized by 1H-NMR, IR, and UV spectroscopy. ANP-PEG was grafted to dimethyldichlorosilane-coated glass (DDS-glass) by photolysis without any premodification of the surface. The effects of various grafting factors, such as the polymer adsorption time, concentration of ANP-PEG, and UV irradiation time, on the PEG grafting efficiency were examined. The PEG-grafted DDS-glass was characterized by measuring surface free energies, surface-induced platelet activation, and the relative amount of PEG grafted on the surface using electron spectroscopy for chemical analysis (ESCA). Platelet adhesion and activation was analyzed by measuring the number and spread area of adherent platelets. The results showed that ANP-PEG had to be adsorbed onto DDS-glass for at least 12 h before photolysis for the maximum grafting efficiency. No platelets could adhere to the PEG-grafted DDS-glass, if the bulk concentration of ANP-PEG in the adsorption solution was between 1 mg/mL and 10 mg/mL. Above 10 mg/mL, platelet activation gradually increased and reached the maximum at 30 mg/mL. Our data indicate that the grafting of ANP-PEG requires careful control of the grafting conditions and that the grafted PEG can prevent surface-induced platelet activation.

12-[(5-iodo-4-azido-2-hydroxybenzoyl)amino]dodecanoic acid: biological recognition by cholesterol esterase and acyl-CoA:cholesterol O-acyltransferase

Potential probes of protein cholesterol and fatty acid binding sites, namely, 12-[(5-iodo-4-azido-2-hydroxybenzoyl)amino]dodecanoate (IFA) and its coenzyme A (IFA:CoA) and cholesteryl (IFA:CEA) esters, were synthesized. These radioactive, photoreactive lipid analogues were recognized as substrates and inhibitors of acyl-CoA:cholesterol O-acyltransferase (ACAT) and cholesterol esterase, neutral lipid binding enzymes which are key elements in the regulation of cellular cholesterol metabolism. In the dark, IFA reversibly inhibited cholesteryl [14C]oleate hydrolysis by purified bovine pancreatic cholesterol esterase with an apparent Ki of 150 microM. Cholesterol esterase inhibition by IFA became irreversible after photolysis with UV light and oleic acid (1 mM) provided 50% protection against inactivation. Incubation of homogeneous bovine pancreatic cholesterol esterase with IFA:CEA resulted in its hydrolysis to IFA and cholesterol, indicating recognition of IFA:CEA as a substrate by cholesterol esterase. The coenzyme A ester, IFA:CoA, was a reversible inhibitor of microsomal ACAT activity under dark conditions (apparent Ki = 20 microM), and photolysis resulted in irreversible inhibition of enzyme activity with 87% efficiency. IFA:CoA was also recognized as a substrate by both liver and aortic microsomal ACATs, with resultant synthesis of 125IFA:CEA. IFA and its derivatives, IFA:CEA and IFA:CoA, are thus inhibitors and substrates for cholesterol esterase and ACAT. Biological recognition of these photoaffinity lipid analogues will facilitate the identification and structural analysis of hitherto uncharacterized protein lipid binding sites.

Identification of a human protein that interacts with nuclear localization signals

Through a series of label transfer experiments, we have identified a HeLa cell nuclear protein that interacts with nuclear localization signals (NLSs). The protein has a molecular weight of 66,000 and an isoelectric point of approximately 6. It associates with a synthetic peptide that contains the SV-40 T antigen NLS peptide but not with an analogous peptide in which an asparagine is substituted for an essential lysine (un-NLS peptide). In addition to these peptides, several proteins have been tested as label donors. With the proteins, there is a correlation between nuclear localization (assayed with lysolecithin-permeabilized cells) and label transfer to the 66-kD protein. The NLS peptide (but not the un-NLS peptide) competes with the proteins in label transfer experiments, but neither wheat germ agglutinin nor ATP has an effect. These results suggest that the 66-kD protein functions as an NLS receptor in the first step of nuclear localization. In the course of this work, we have observed that the Staphylococcus aureus protein A is a strongly karyophilic protein. Its dramatic nuclear localization properties suggest that it may have multiple copies of an NLS.

Proteins associated with activity of Fc receptors on isolated human placental syncytiotrophoblast microvillous plasma membranes

To identify Fc receptors from human placental microvilli, proteins that were liberated by detergents from human placental synctiotrophoblast microvillous membranes (StMPM) were characterized by their abilities to bind human IgG in immune complexes with sheep or goat anti-human IgG and to monomeric rabbit anti-dinitrophenol (DNP) IgG bound to DNP-lysine Sepharose. Three placental IgG-binding proteins coprecipitated with immune complexes (Mr = 68,000, 52,000-56,000, 40,000) and were designated pIBP68, pIBP56 and pIBP40, respectively. Of the three proteins only pIBP56 bound to immobilized monomeric rabbit IgG. It was isolated from detergent lysates of StMPM and LDS/phenol glycoprotein extracts of placental plasma membranes suggesting that pIBP56 was a glycoprotein FcR previously reported (Mikulska et al, 1982). The binding specificities of pIBP56 and pIBP40 appeared to be detergent dependent. Photoaffinity crosslinking of StMPM surface proteins in situ to monomeric rabbit derivatized with N-succinimidyl(4-azidophenyl)-I, 3-dithiopropionate identified IgG-binding proteins identical in size to pIBP56 and pIBP40. Crosslinking further suggested that monomeric IgG covalently bound to a complex of StMPM proteins with a total size of 110,000-120,000 Mr. The findings suggest that pIBP68, pIBP56 and pIBP68 are responsible for IgG binding activity of placental StMPM.

The use of sulfosuccinimidyl-2-(p-azidosalicylamido)-1,3'-dithiopropionate as a crosslinking reagent to identify cell surface receptors

Conditions for solubilizing and iodinating the heterobifunctional thiol-cleavable photoreactive crosslinking reagent sulfosuccinimidyl-2-(p-azidosalicylamido)-1,3'-dithiopropionate which leave the ester moiety, disulfide bond, and azido group reactive are described. Iodination was performed in a mixture of dimethyl sulfoxide and bicarbonate, pH 9.0 (1:20, v/v), as solubilizing agent and Iodogen as oxidant. The lectin phytohemagglutinin was derivatized with the iodinated crosslinker and the interaction between phytohemagglutinin and mononuclear cells was chosen as the model system to monitor the efficiency of sulfosuccinimidyl-2-(p-azidosalicylamido)-1,3'-dithiopropionate as a crosslinking reagent. Transfer of 125I to the biologically significant T11 lymphocyte receptor in addition to 125I labeling of other membrane proteins to which the lectin binds was detected by polyacrylamide gel electrophoresis under reducing conditions.

Use of the photoaffinity cross-linking agent N-hydroxysuccinimidyl-4-azidosalicylic acid to characterize salivary-glycoprotein-bacterial interactions

The present study has utilized the iodinatable cross-linking agent N-hydroxysuccinimidyl-4-azidosalicylic acid (ASA) to examine the specific interaction between the proline-rich glycoprotein (PRG) of human parotid saliva and Streptococcus sanguis G9B. The binding of 125I-ASA-PRG to Streptococcus sanguis G9B displayed saturation kinetics, reversibility and was inhibited by unlabelled PRG. Inhibition studies with other glycoproteins and saccharides indicated that binding was mediated by a bacterial adhesin with specificity towards N-acetylneuraminic acid, galactose, and N-acetylgalactosamine. After cross-linking, the 125I-ASA-PRG-adhesin complex could be extracted with SDS and separated from uncoupled 125I-ASA-PRG by gel filtration on Sepharose CL-6B. Approx. 1% of the 125I-ASA-PRG was cross-linked to the bacterial surface. Examination of the 125I-ASA-PRG-adhesin complex by SDS/polyacrylamide-gel electrophoresis/fluorography on 5% -(w/v)-polyacrylamide gels revealed that PRG was bound to two bacterial components. These findings support our previous suggestion that human salivary glycoproteins can specifically interact with oral streptococci and that these interactions occur between the glycoprotein's carbohydrate units and lectin(s) on the bacterial cell surface.

Photochemical cross-linking of protein and DNA in chromatin. Synthesis and application of a photosensitive cleavable derivative of 9-aminoacridine with two photoprobes connected through a disulphide-containing linker

A novel cleavable photo-cross-linking reagent, N-(2-methoxy-6-azidoacridin-9-yl)-N'-(4-azidobenzoyl)cystamine, for analysis of protein-nucleic acid interactions, has been synthesized. The reagent contains two photosensitive groups that can be activated sequentially. The azidoacridinyl moiety is sensitive to u.v. and visible light (lambda less than or equal to 450 nm), whereas the azidobenzoyl part needs higher-energy light (lambda less than or equal to 350 nm). Furthermore, the disulphide bridge connecting the two photoactive groups can be cleaved by reduction with mercaptans. The reagent is shown to induce cleavable cross-links between all five major histones and DNA in chromatin from Ehrlich ascites cells on activation with long-wavelength u.v. light (lambda greater than 300 nm) at an efficiency of approximately 3% of the added reagent.

Synthesis and application of two reagents for the introduction of sulfhydryl groups into proteins

Two reagents are described which can be used for the introduction of sulfhydryl groups into proteins. Mercaptopropionylhydrazide modifies specifically periodate-oxidized N termini of proteins, provided that the N-terminal residue is serine or threonine. 3-(Phenyldithio)propionimidate introduces a disulfide bond at lysine residues of proteins. Reduction converts the disulfide into a sulfhydryl group. The imidate compound was found to react with a high specificity with only one lysine residue of ribosomal protein L7/L12.