Improving SH3 domain ligand selectivity using a non-natural scaffold

BACKGROUND: Src homology 3 (SH3) domains bind sequences bearing the consensus motif PxxP (where P is proline and x is any amino acid), wherein domain specificity is mediated largely by sequences flanking the PxxP core. This specificity is limited, however, as most SH3 domains show high ligand cross-reactivity. We have recently shown that diverse N-substituted residues (peptoids) can replace the prolines in the PxxP motif, yielding a new source of ligand specificity. RESULTS: We have tested the effects of combining multiple peptoid substitutions with specific flanking sequences on ligand affinity and specificity. We show that by varying these different elements, a ligand can be selectively tuned to target a single SH3 domain in a test set. In addition, we show that by making multiple peptoid substitutions, high-affinity ligands can be generated that completely lack the canonical PxxP motif. The resulting ligands can potently disrupt natural SH3-mediated interactions. CONCLUSIONS: Peptide-peptoid hybrid scaffolds yield SH3 ligands with markedly improved domain selectivity, overcoming one of the principal challenges in designing inhibitors against these domains. These compounds represent important leads in the search for orthogonal inhibitors of SH3 domains, and can serve as tools for the dissection of complex signaling pathways.     

Dithiodiglycolamide: novel ligand with highest selectivity and extractability for palladium

A novel multidentate ligand N,N,N′,N′-tetra(2-ethylhexyl) dithiodiglycolamide DTDGA has been synthesized and studied for its extraction behavior towards various elements present in high level liquid waste (HLW). The extractant showed remarkable extractability and selectivity for palladium vis a vis other metal ions present in HLW. The distribution ratio as well as the separation factor for palladium was found to be the highest reported so far thus making this extractant one of the most promising candidates for effective separation of palladium from HLW.     

Amphiphilic copolymers with increased affinity for substrates

The copolymers of methyl quaternized 2-dimethylaminoethyl acrylate and styrene, 2-vinyl naphthalene, acrylic acid iso-octyl ester, or acrylic acid n-butyl ester have been prepared. Studies were made of the binding of a “binding probe,” methyl orange, by the copolymers in aqueous solution. The first binding constants and the thermodynamic parameters in the course of the binding were evaluated. Furthermore, the intensity of fluorescence of a hydrophobic fluorescent probe, 2-p-toluidinylnaphthalene-6-sulfonate, in the presence of these polymers was investigated. In addition, the fluorescence spectra of monomer and excimer emissions of the polymers with aromatic residues were measured. The excimer/monomer fluorescence intensity ratio was studied in the presence of various additives such as methyl orange, urea, methanol, and NaCl to gain an insight into the nature of microdomains in the polymer. The nature and phenomena of dye binding and hydrophobic fluorescent probe binding with the polymers are discussed. © 1993 John Wiley & Sons, Inc.     

New nanostructured heterogeneous catalysts with increased selectivity and stability

In this perspective, several examples of work from our laboratory are reported where colloidal or self-assembly chemistry has been used to design new catalysts with specific properties. In the first, platinum nanoparticles with well-defined shapes have been dispersed on a high-surface-area silica support in order to take advantage of the structure sensitivity exhibited by the interconversion between the cis and trans isomers of olefins. The second case involves the use of dendrimers as scaffolding structures to prepare catalysts with small platinum nanoparticles of well-defined size. Reduced sintering of metal nanoparticles on supported catalysts is accomplished in our third example via their encapsulation inside a layer of mesoporous silica deposited on top, after metal dispersion, and etched using a newly developed surface-protection process. The final project refers to the use of yolk@shell metal-oxide systems as nanoreactors for photocatalysis. In all those examples, new synthetic nanotechnology has been directed to address a specific issue in catalysis previously identified by surface-science studies.     

Platinum squares with high selectivity and affinity for human telomeric G-quadruplexes

Two new Pt(II) squares with quinoxaline-bridges selectively stabilize human telomeric G-quadruplexes with high binding constants (10(7)-10(9) M(-1)) and an unprecedented binding stoichiometric ratio of Pt(II) square/G-quadruplex (6 : 1). This selectivity is likely due to the Pt(II) squares' cube-like shape. Both Pt(II) squares also show significant telomerase inhibition and anticancer efficacy.     

Novel artificial receptors for alkylammonium ions with remarkable selectivity and affinity

The benzene-based tripodal tris(oxazolines) have been developed as the most selective and strong receptors toward linear alkylammonium ions reported to date. Among six tris(oxazolines) based on 2,4,6-trimethylbenzene framework, the phenylglycinol-derived receptor 4 exhibits the largest association constant toward nBuNH3+ (logK(ass) = 6.65 +/- 0.02), while a similar value toward tBuNH3+, (logK(ass) = 3.80 +/- 0.01) compared with others, which corresponds to the selectivity ratio of nBuNH3+/tBuNH3+ as high as approximately equals 700. The tris(oxazoline) 6 that has bare oxazoline ring exhibits still a large association constant toward sterically hindered tBuNH3+ (logK(ass) = 5.26 +/- 0.02). Both receptors 4 and 6 extract beta-phenethylammonium ion from water into chloroform almost completely. When the benzene frame is changed from 2,4,6-trimethylbenzene to 2,4,6-triethylbenzene, dramatic changes in the affinity as well as in the selectivity are observed. The association constant observed by tris(oxazoline) 8 toward nBuNH3+ approaches 10(8)M(-1) and the selectivity ratio of nBuNH3+/tBuNH3+ is increased to 2,700. This selectivity is even more enhanced to 4,000 with tris(oxazoline) 9. The enhanced binding affinity and high selectivity observed with receptors 4 and related derivatives 7-9 compared with others can be explained by an optimized steric and electronic environment provided by the phenyl substituents, which has been unambiguously demonstrated by X-ray crystallographic and 1H NMR spectroscopic studies on the host-guest complexes. The new receptor system has several unique features such as ready availability, structural simplicity, and in particular, versatility in derivatization. By virtue of these advantages, it can be readily tailored as selective receptors toward biologically important amines.     

New trends in affinity sensing: aptamers for ligand binding

Aptamers are artificial nucleic acid ligands that can be generated against amino acids, drugs, proteins and other molecules. They are isolated from complex libraries of synthetic nucleic acids by an iterative process of adsorption, recovery and amplification. This review described the in vitro process to obtain aptamers (SELEX). It mentions the main characteristics of these molecules (i.e. affinity, specificity and stability). Moreover, it discusses advantages over antibodies. It reports potential applications of aptamers in analytical and diagnostic assays as biocomponents of biosensors (aptasensors) and allosteric ribozymes (aptazymes).     

Assessment of programs for ligand binding affinity prediction

The prediction of the binding free energy between a ligand and a protein is an important component in the virtual screening and lead optimization of ligands for drug discovery. To determine the quality of current binding free energy estimation programs, we examined FlexX, X-Score, AutoDock, and BLEEP for their performance in binding free energy prediction in various situations including cocrystallized complex structures, cross docking of ligands to their non-cocrystallized receptors, docking of thermally unfolded receptor decoys to their ligands, and complex structures with "randomized" ligand decoys. In no case was there a satisfactory correlation between the experimental and estimated binding free energies over all the datasets tested. Meanwhile, a strong correlation between ligand molecular weight-binding affinity correlation and experimental predicted binding affinity correlation was found. Sometimes the programs also correctly ranked ligands' binding affinities even though native interactions between the ligands and their receptors were essentially lost because of receptor deformation or ligand randomization, and the programs could not decisively discriminate randomized ligand decoys from their native ligands; this suggested that the tested programs miss important components for the accurate capture of specific ligand binding interactions.     

Tether-controlled cycloadditions for the asymmetric synthesis of decalins: increased selectivity in acetonitrile solvent

[reaction: see text] The beneficial influence of cis-isopropylidene acetal tether control groups, to facilitate the asymmetric synthesis of substituted decalins by intramolecular Diels-Alder reactions, is described. Compared to trans-acetonides, these cases proceed under milder conditions to afford the cis-fused adducts from an endo transition state. An unusual acetonitrile solvent effect exerts a dramatic influence on the diastereoselectivity. This strategy leads to the chiral nonracemic bicyclo[4.4.0]decane core of diverse natural products.     

CuAAC macrocyclization: high intramolecular selectivity through the use of copper-tris(triazole) ligand complexes

A range of multivalent heteroaryl ligands, copper sources, and solvent systems have been investigated for use in CuAAC-mediated macrocyclization reactions. These studies have revealed the key factors governing selectivity for macrocyclization versus dimerization and identified a simple but specific set of reaction conditions capable of efficiently generating a diverse series of drug-like macrocycles at modest dilution in up to 95% yield.     

Contributions of commercial sorbents to the selectivity in immobilized metal affinity chromatography with Cu(II)

Immobilized copper(II) affinity chromatography [Cu(II)-immobilized metal affinity chromatography (IMAC)] has been used in proteomics to simplify sample mixtures by selecting histidine-containing peptides from proteolytic digests. This paper examines the specificity of four different support materials with an iminodiacetic acid (IDA) stationary phase in the selection of only histidine-containing peptides in the single step capture-release mode. Three of the sorbents examined were commercially available: HiTrap Chelating HP (agarose), TSK Chelate-5PW, and Poros 20MC. IDA was also immobilized on CIM discs (monolithic glycidylmethacrylate-ethylene dimethacrylate). Tryptic digests of transferrin and beta-galactosidase were used as model samples to evaluate these sorbents. It was found that among the examined matrices, the TSK Chelate-5PW sorbent bound histidine-containing peptides the strongest, while Poros matrix was found to have a high degree of non-specific bindings. Agarose-based columns showed relatively high selectivity and specificity.     

Structure-based approach for the study of estrogen receptor binding affinity and subtype selectivity

Estrogens exert important physiological effects through the modulation of two human estrogen receptor (hER) subtypes, alpha (hERalpha) and beta (hERbeta). Because the levels and relative proportion of hERalpha and hERbeta differ significantly in different target cells, selective hER ligands could target specific tissues or pathways regulated by one receptor subtype without affecting the other. To understand the structural and chemical basis by which small molecule modulators are able to discriminate between the two subtypes, we have applied three-dimensional target-based approaches employing a series of potent hER-ligands. Comparative molecular field analysis (CoMFA) studies were applied to a data set of 81 hER modulators, for which binding affinity values were collected for both hERalpha and hERbeta. Significant statistical coefficients were obtained (hERalpha, q(2) = 0.76; hERbeta, q(2) = 0.70), indicating the internal consistency of the models. The generated models were validated using external test sets, and the predicted values were in good agreement with the experimental results. Five hER crystal structures were used in GRID/PCA investigations to generate molecular interaction fields (MIF) maps. hERalpha and hERbeta were separated using one factor. The resulting 3D information was integrated with the aim of revealing the most relevant structural features involved in hER subtype selectivity. The final QSAR and GRID/PCA models and the information gathered from 3D contour maps should be useful for the design of novel hER modulators with improved selectivity.     

Carbon-fiber microelectrodes modified with 4-sulfobenzene have increased sensitivity and selectivity for catecholamines

Elliptical and cylindrical geometries of carbon-fiber microelectrodes were modified by covalent attachment of 4-sulfobenzenediazonium tetrafluoroborate following its electroreduction. Elliptical electrodes fabricated from Thornel P-55 carbon fibers show the highest amount of 4-sulfobenzene attached to the electrode. Fast-scan cyclic voltammetry was used to compare the response to dopamine and other neurochemicals at these modified carbon-fiber microelectrodes. The grafted layer causes an increased sensitivity to dopamine and other positively charged analytes that is due to increased adsorption of analyte in the grafted layer. However, this layer remains permeable to negatively charged compounds. Modified electrodes retain the increased sensitivity for dopamine during measurements in mouse brain tissue.     

Molecular recognition of protein surfaces: high affinity ligands for the CBP KIX domain

Potent and specific inhibitors of protein.protein interactions have potential both as therapeutic compounds and biological tools, yet discovery of such molecules remains a challenge. Our laboratory has recently described a strategy, called protein grafting, for the identification of miniature proteins that bind protein surfaces with high affinity and specificity and inhibit the formation of protein.protein complexes. In protein grafting, those residues that comprise a functional alpha-helical binding epitope are stabilized on the solvent-exposed alpha-helical face of the small yet stable protein avian pancreatic polypeptide (aPP). Here we use protein grafting in combination with molecular evolution by phage display to identify phosphorylated peptide ligands that recognize the shallow surface of CBP KIX with high nanomolar to low micromolar affinity. Furthermore, we show that grafting of the CBP KIX-binding epitope of CREB KID onto the aPP scaffold yields molecules capable of high affinity recognition of CBP KIX even in the absence of phosphorylation. Importantly, both classes of designed ligands exhibit high specificity for the target CBP KIX domain over carbonic anhydrase and calmodulin, two unrelated proteins that bind hydrophobic or alpha-helical molecules that might be encountered in vivo.     

Selection of modified oligonucleotides with increased target affinity via MALDI-monitored nuclease survival assays

Reported here is how modified oligonucleotides with increased affinity for DNA or RNA target strands can be selected from small combinatorial libraries via spectrometrically monitored selection experiments (SMOSE). The extent to which target strands retard the degradation of 5'-acyl-, 5'-aminoacyl-, and 5'-dipeptidyl-oligodeoxyribonucleotides by phosphodiesterase I (EC 3.1.4.1) was measured via quantitative MALDI-TOF mass spectrometry. Oligonucleotide hybrids were prepared on solid support, and nuclease selections were performed with up to 10 modified oligonucleotides in one solution. The mass spectrometrically monitored experiments required between 120 and 300 pmol of each modified oligonucleotide, depending on whether HPLC-purified or crude compounds were employed. Data acquisition and analysis were optimized to proceed in semiautomated fashion, and functions correcting for incomplete degradation during the monitoring time were developed. Integration of the degradation kinetics provided "protection factors" that correlate well with melting points obtained with traditional UV melting curves employing single, pure compounds. Among the components of the five libraries tested, three were found to contain 5'-substituents that strongly stabilize Watson--Crick duplexes. Selecting and optimizing modified oligonucleotides via monitored nuclease assays may offer a more efficient way to search for new antisense agents, hybridization probes, and biochemical tools.