A study of Src SH2 domain protein-phosphopeptide binding interactions by electrospray ionization mass spectrometry

The noncovalent binding of various peptide ligands to pp60^src (Src) SH2 (Src homology 2) domain protein (12.9 ku) has been used as a model system for development of electrospray ionization mass spectrometry (ESI-MS) as a tool to study noncovalently bound complexes. SH2 motifs in proteins are critical in the signal transduction pathways of the tyrosine kinase growth factor receptors and recognize phosphotyrosine-containing proteins and peptides. ESI-MS with a magnetic sector instrument and array detection has been used to detect the protein-peptide complex with low-picomole sensitivity. The relative abundances of the multiply charged ions for the complex formed between Src SH2 protein and several nonphosphorylated and phosphorylated peptides have been compared. The mass spectrometry data correlate well to the measured binding constants derived from solution-based methods, indicating that the mass spectrometry-based method can be used to assess the affinity of such interactions. Solution-phase equilibrium constants may be determined by measuring the amount of bound and unbound species as a function of concentration for construction of a Scatchard graph. ESI-MS of a solution containing Src SH2 with a mixture of phosphopeptides showed the expected protein-phosphopeptide complex as the dominant species in the mass spectrum, demonstrating the method’s potential for screening mixtures from peptide libraries.     

Structure-based design and solid-phase parallel synthesis of phosphorylated nonpeptides to explore hydrophobic binding at the Src SH2 domain

Using a novel, solid-phase parallel synthetic route and a computational docking program, a series of phosphorylated nonpeptides were generated to determine their structure-activity relationships (SAR) for binding at the SH2 domain of pp60src (Src). A functionalized benzoic acid intermediate was attached to solid support via Rink amide linkage, which upon acid cleavage generated the desired benzamide template-based nonpeptides in a facile manner. Compounds were synthesized using a combination of solid- and solution-phase techniques. Purification using reversed-phase, semipreparative HPLC allowed for quantitative SAR studies. Specifically, this work focused on functional group modifications, in a parallel fashion, designed to explore hydrophobic binding at the pY+3 pocket of the Src SH2 domain.     

Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding.

Isothermal titration calorimetry and X-ray crystallography have been used to determine the structural and thermodynamic consequences associated with constraining the pTyr residue of the pYEEI ligand for the Src Homology 2 domain of the Src kinase (Src SH2 domain). The conformationally constrained peptide mimics that were used are cyclopropane-derived isosteres whereby a cyclopropane ring substitutes to the N-Calpha-Cbeta atoms of the phosphotyrosine. Comparison of the thermodynamic data for the binding of the conformationally constrained peptide mimics relative to their equivalent flexible analogues as well as a native tetrapeptide revealed an entropic advantage of 5-9 cal mol(-1) K(-1) for the binding of the conformationally constrained ligands. However, an unexpected drop in enthalpy for the binding of the conformationally constrained ligands relative to their flexible analogues was also observed. To evaluate whether these differences reflected conformational variations in peptide binding modes, we have determined the crystal structure of a complex of the Src SH2 domain bound to one of the conformationally constrained peptide mimics. Comparison of this new structure with that of the Src SH2 domain bound to a natural 11-mer peptide (Waksman et al. Cell 1993, 72, 779-790) revealed only very small differences. Hence, cyclopropane-derived peptides are excellent mimics of the bound state of their flexible analogues. However, a rigorous analysis of the structures and of the surface areas at the binding interface, and subsequent computational derivation of the energetic binding parameters, failed to predict the observed differences between the binding thermodynamics of the rigidified and flexible ligands, suggesting that the drop in enthalpy observed with the conformationally constrained peptide mimic arises from sources other than changes in buried surface areas, though the exact origin of the differences remains unclear.     

SH2 binding site comparison: a new application of the SURFCOMP method

To avoid side effects, it is often desirable to increase the specificity of a drug candidate when targeting one member of a family of related proteins, whereby one exploits small differences between the structures of the binding sites. Identification of such differences can be carried out by analyzing the distributions of physicochemical properties mapped onto molecular surfaces. Here we demonstrate that SURFCOMP, our local surface similarity detection method, is able to detect differences between the binding sites of two closely related proteins. We analyzed the SH2 domains of Sap and Eat-2, two highly similar signal transduction molecules involved in inflammatory processes and found differences between their binding sites that can possibly lead to a better understanding of the different specificities of the two proteins.     

A new host compound for the selective inclusion of ethanol

A new host compound of the onium salt type,N-(3-biphenylmethyl)quininium bromide (1), is described. This host compound shows an unusually high selectivity for the inclusion of ethanol. Using this clathrand, ethanol can be extracted from a variety of solvent mixtures. In most cases, a remarkable enrichment of the ethanol is observed. The following solvents in a mixture with ethanol remain in the mother liquid: methanol,n-propanol,n-hexane, pyridine.     

A triazine compound S06 inhibits proinvasive crosstalk between carcinoma cells and stromal fibroblasts via binding to heat shock protein 90

Carcinoma-associated fibroblasts (CAFs) promote tumor invasion by secreting soluble factors. A tagged triazine library was screened in our novel transwell coculture model of CAF and oral squamous cell carcinoma (OSCC). We discovered compound S06, which reduced OSCC invasion by inhibiting secretion of CAF-derived proinvasive chemokines. The N-terminus of Hsp90 was found to be the cellular target of S06. Importantly, S06 did not induce hepatic toxicity, a side effect associated with well-known Hsp90 inhibitors. Moreover, S06 inhibited tumor cell migration in a zebrafish xenograft model. Our results demonstrate that Hsp90 is a novel target for stromal-based therapy to modulate proinvasive molecular crosstalk within the tumor microenvironment. Furthermore, S06 represents a new class of Hsp90 inhibitor and is an attractive candidate for anticancer drug development.     

High level ab initio and density functional theory study of bond selective dissociation of CH3SH and CH3CH2SH radical cations

Selective bond dissociation energies for CH₃SH and CH₃CH₂SH radical cations were evaluated with G1, G2, G2MP2, B3LYP, BLYP, and SVWN computational methods. It was determined that both G2 and CBSQ evaluate very accurate bond dissociation energies for thiol radical cations, while gradient-corrected BLYP computes the best energies of three employed DFT methods. For the CH₃CH₂SH radical cation, new, higher than previously estimated selective bond dissociation energies were suggested. Received: 10 September 1997 / Accepted: 9 September 1998 / Published online: 11 November 1998     

Ab initio molecular-orbital study of the binding of ZnII with SH2 and SH−

This paper reports an ab initio molecular-orbital (MO ) study of binding of SH₂ and SH^? with Zn^II. The mechanism of binding of Zn^II with these ligands is investigated using a detailed analysis of the energy decomposition and of the electronic distribution. The dependence of the results on the choice of the basis set for sulfur (in particular the effect of incorporation of diffuses p and d orbitals) on the geometry of ligand binding, the binding energy, and the proton affinity of SH^? are investigated. Comparison made with the corresponding results concerning the binding of OH₂, OH^?, and NH₃ shows that sulfur binding is less favorable although more covalent. Both sulfur ligands show a marked preference for angular conformations for binding with the metal ion. The effect of Zn^II binding on the ease of deprotonation of H₂S is quite similar to the corresponding effect found earlier for H₂O.     

A phosphoarginine containing peptide as an artificial SH2 ligand

We have developed a synthesis of phosphoarginine containing peptides using a bis(2,2,2-trichloroethyl) protected phosphoarginine derivative as building block. Binding studies and computer modelling demonstrate the ability of the SH2 domain from Src kinase to recognize a phosphoarginine-containing peptide in a phosphoryl group-dependent manner.     

Synthesis of 2-phenylbenzofuran derivatives and selective binding activities on estrogen receptor

An improved chemical reaction protocol with short time and easy work-up was described here for 2-phenylbenzofuran derivatives. The final purified products, 2-phenylbenzofuran derivatives 5a-g and the intermediate diols 4a-g, were evaluated for their estrogen receptor (ER) binding affinity and selective activity in vitro. Among these fourteen tested compounds, 4g and 5g showed higher binding affinity on ER subtypes, ERα and ERβ. Compound 4g exhibited preferable ERα binding, while 5g was more estrogen selective for ERβ. The molecular docking was also performed to explore the detailed interactive interface between ER and the compounds.     

Resonant 2-photon ionization study of the conformation and the binding of water molecules to 2-phenylethanethiol (PhCH2CH2SH)

The structures of 2-phenylethanethiol (PET, PhCH(2)CH(2)SH) and its 1:1 water clusters have been studied using resonant two-photon ionization spectroscopy including band contour analysis and UV-UV holeburning, combined with extensive ab initio calculations on ground and excited states. The most populated conformer, labeled Ggpi, has a gauche arrangement about the SCCC and HSCC bonds that permits a stabilizing SH...dpi type of hydrogen bond. The other observed conformer, Ag, is anti with respect to the SCCC bond. In the dominant 1:1 water cluster, a water molecule binds to the Ggpi conformer via an OH...S hydrogen bond and two significant CH...O interactions. There is also evidence for water binding to conformer Ag with a similar arrangement, and for a second Ggpi cluster where water inserts between the SH and the aromatic ring. The additional interactions to the water molecules result in net D(e) binding energies approximately double those resulting from a single thiol-water hydrogen bond. The (1)(pi,pi(*)) excited state lifetimes in the bare molecules are very short because of internal conversion to a dissociative (1)(n,pi(*)) state related to the thiol. In the dominant Gw(1) cluster, the lifetime is significantly increased from <1 to approximately 4 ns. Hydrogen bonding to the thiol, which raises the energy of the dissociative (1)(n,pi(*)) state, accounts for this behavior.     

A new half-condensed Schiff base compound: highly selective and sensitive pH-responsive fluorescent sensor

A new probe, 3-[(3-benzyloxypyridin-2-ylimino)methyl]-2-hydroxy-5-methylbenzaldehyde (1-H) behaves as a highly selective fluorescent pH sensor in a Britton-Robinson buffer at 25 °C. The pH titrations show a 250-fold increase in fluorescence intensity within the pH range of 4.2 to 8.3 with a pK(a) value of 6.63 which is valuable for studying many of the biological organelles.     

A highly selective naked-eye probe for hypochlorite with the p-methoxyphenol-substituted aniline compound

A highly selective naked-eye detection of ClO⁻ is successfully established with probe 1 by taking advantage of the oxidation transformation of p-methoxyphenol into benzoquinone with ClO⁻ and the ICT absorption within the electron donor-acceptor compound. The color of the solution of probe 1 was changed, obviously upon addition of ClO⁻ and ClO⁻ with concentration as low as 1.74 μM can be analyzed in aqueous solution with probe 1. Moreover, the interferences of other anions can be neglected.     

CdIn2S2Se2: A new semiconducting compound

The optical and electrical properties of CdIn₂S₂Se₂, a new layered semiconducting compound, were examined in the temperature range 10–300 K. The absorption edge at room temperature is observed at 1.95 eV, with a temperature shift of about 4.6 × 10⁻⁴ eV/K. Electrical transport is due to electrons, whose temperature independent density is about 3 × 10¹⁷ cm⁻³. The room-temperature mobility is 130 cm²/Vs, independent of the conduction direction. However, measurements parallel and perpendicular to c-axis show different linear decreases of the mobility with reciprocal temperature. Au/CdIn₂S₂Se₂/In Schottky diodes were produced.     

A new selective preparation of ethyl 7-aminopteridine-6- carboxylate derivatives and related compound

A series of ethyl 7-amino-2,4-dioxopteridine-6-carboxylates 4 and ethyl 7-amino-4-oxo-2-thioxopteridine-6-carboxylates 5 , of interest biologically, has been prepared in one step from the reaction of such vicinal-diamines as 1,3-dialkyl-5,6-diaminouracils 2 or 1,3-dialkyl-5,6-diamino-2-thiouracils 3 with diethyl (E)-2,3-dicyanobutenedioate ( 1 ). Moreover, ethyl 3-amino[1,2,4]triazino[2,3-a]-1H-benzimidazole-2-carboxylate ( 11 ) was also obtained from the reaction between 1,2-diamino-1H-benzimidazole ( 10 ) and 1 . The structural studies of 4, 5 , and 11 prepared were carried out by nmr experiments in some details.     

A new FeII quaterpyridyl M4L6 tetrahedron exhibiting selective anion binding

A rigid linear bis-bidentate quaterpyridine undergoes metal directed self-assembly with iron(ii) salts yielding M(4)L(6) host-guest complexes; selective anion binding for PF(6)(-) over BF(4)(-) is observed.     

A general technique to rank protein-ligand binding affinities and determine allosteric versus direct binding site competition in compound mixtures

To realize the full potential of combinatorial chemistry-based drug discovery, generic and efficient tools must be developed that apply the strengths of diversity-oriented chemical synthesis to the identification and optimization of lead compounds for disease-associated protein targets. We report an affinity selection-mass spectrometry (AS-MS) method for protein-ligand affinity ranking and the classification of ligands by binding site. The method incorporates the following steps: (1) an affinity selection stage, where protein-binding compounds are selected from pools of ligands in the presence of varying concentrations of a competitor ligand, (2) a first chromatography stage to separate unbound ligands from protein-ligand complexes, and (3) a second chromatography stage to dissociate the ligands from the complexes for identification and quantification by MS. The ability of the competitor ligand to displace a target-bound library member, as measured by MS, reveals the binding site classification and affinity ranking of the mixture components. The technique requires no radiolabel incorporation or direct biochemical assay, no modification or immobilization of the compounds or target protein, and all reaction components, including any buffers or cofactors required for protein stability, are free in solution. We demonstrate the method for several compounds of wide structural variety against representatives of the most important protein classes in contemporary drug discovery, including novel ATP-competitive and allosteric inhibitors of the Akt-1 (PKB) and Zap-70 kinases, and previously undisclosed antagonists of the M(2) muscarinic acetylcholine receptor, a G-protein coupled receptor (GPCR). The theoretical basis of the technique is analyzed mathematically, allowing quantitative estimation of binding affinities and, in the case of allosteric interaction, absolute determination of binding cooperativity. The method is readily applicable to high-throughput screening hit triage, combinatorial library-based affinity optimization, and developing structure-activity relationships among multiple ligands to a given receptor.