Chimeric (alpha/beta + alpha)-peptide ligands for the BH3-recognition cleft of Bcl-XL: critical role of the molecular scaffold in protein surface recognition

Molecules that bind to specific surface sites on proteins are of great interest from both fundamental and practical perspectives. We are exploring a ligand development strategy that is based on oligomers with discrete folding propensities ("foldamers"); we target a specific cleft on the cancer-associated protein Bcl-xL because this system is well characterized structurally. In vivo, this cleft binds to alpha-helical segments (BH3 domains) of other proteins. We evaluated several types of helical foldamer, built entirely from beta-amino acid residues or from mixtures of alpha- and beta-amino acid residues, and ultimately identified foldamers in the latter class that bind very tightly to Bcl-xL. Our results suggest that combining different types of foldamer backbones will be an effective and general strategy for creating high-affinity and specific ligands for protein surface sites.     

Novel malonamide derivatives as alpha v beta 3 antagonists. Syntheses and evaluation of 3-(3-indolin-1-yl-3-oxopropanoyl)aminopropanoic acids on vitronectin interaction with alpha v beta 3.

In attempt to find novel integrin alphavbeta3 antagonists, we selected SC65811 and its guanidine analogue (1) as lead compounds. Modification of the glycine part of SC65811 led to a new series of malonamide derivatives that exhibited alphavbeta3 inhibitory activity. Among them, (R,S)-3-[3-[6-(3-benzylureido)indolin-1-yl]-3-oxopropanoylamino]-3- (pyridin-3-yl)propanoic acid (43a) showed not only potent activity with an IC50 value of 3.0 nM but also good selectivity for alphavbeta3 relative to alphaIIbbeta3, alpha5beta1, and alphavbeta5 with IC50 values of 19,000, 11,000, and 14 nM, respectively. Furthermore, optimization of 43a led to the most potent alphavbeta3 antagonist, (R,S)-3-(3-[6-[(4,5-dihydro-1H-imidazol-2-yl)amino]indolin-1-yl]-3-oxopropanoylamino)-3-(quinolin-3-yl)propanoic acid (431) with an IC50 value of 0.42 nM. The synthesis and the structure-activity relationships of these malonamide derivatives are presented.     

A general and rapid cell-free approach for the interrogation of protein-protein, protein-DNA, and protein-RNA interactions and their antagonists utilizing split-protein reporters

Split-protein reporters have emerged as a powerful methodology for imaging biomolecular interactions which are of much interest as targets for chemical intervention. Herein we describe a systematic evaluation of split-proteins, specifically the green fluorescent protein, beta-lactamase, and several luciferases, for their ability to function as reporters in completely cell-free systems to allow for the extremely rapid and sensitive determination of a wide range of biomolecular interactions without the requirement for laborious transfection, cell culture, or protein purification (12-48 h). We demonstrate that the cell-free split-luciferase system in particular is amenable for directly interrogating protein-protein, protein-DNA, and protein-RNA interactions in homogeneous assays with very high sensitivity (22-1800 fold) starting from the corresponding mRNA or DNA. Importantly, we show that the cell-free system allows for the rapid (2 h) identification of target-site specificity for protein-nucleic acid interactions and in evaluating antagonists of protein-protein and protein-peptide complexes circumventing protein purification bottlenecks. Moreover, we show that the cell-free split-protein system is adaptable for analysis of both protein-protein and protein-nucleic acid interactions in artificial cell systems comprising water-in-oil emulsions. Thus, this study provides a general and enabling methodology for the rapid interrogation of a wide variety of biomolecular interactions and their antagonists without the limitations imposed by current in vitro and in vivo approaches.     

The interactions of added phenanthroline and triphenylphosphine ligands with the copper(I) tetrahydroborates (phen)Cu(BH4) and (phen)(PPh3)Cu(BH4): Probing the character of species in solution

Added free ligand, i.e. phenanthroline for (phen)CuBH₄ and either phenanthroline or triphenylphosphine for (phen)PPh₃CuBH₄, causes a progressive change in the mode of attachment of the η²–BH₄ moiety from that in the initial complexes to the formation in solution of ionic species of the type [(phen)₂Cu]⁺BH₄⁻ and [(phen)(PPh₃)₂Cu]⁺BH₄⁻, respectively. These changes were indicated by: (i) infrared spectroscopy, which showed both a gradual loss of signals attributed to ν(B–H_b) and δ(BH₂) and their replacement with spectra typical of ionic BH₄⁻ ion; (ii) an increase in the conductance measured that was consistent with a 1:1 electrolyte; (iii) chemical shift changes in the ¹¹B- and ³¹P-NMR signals associated with the BH₄⁻ and PPh₃ moieties, respectively and (iv) a relative increase in signal intensities of the ions detected by electrospray mass spectrometry.     

Gd(III) chelates as NMR probes of protein-protein interactions. Case study: rubredoxin and cytochrome c3

Two cyclen-derived Gd probes, [Gd-DOTAM](3+) and [Gd-DOTP](5-) (DOTAM = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetamide; DOTP = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetrakis(methylenephosphonate)), were assessed as paramagnetic relaxation enhancement (PRE)-inducing probes for characterization of protein-protein interactions. Two proteins, Desulfovibrio gigas rubredoxin and Desulfovibrio gigas cytochrome c(3), were used as model partners. In a (1)H NMR titration it was shown that [Gd-DOTP](5-) binds to cytochrome c(3) near heme IV, causing pronounced PREs, characterized by line width broadenings of the heme methyl resonances at ratios as low as 0.08. A K(d) of 23 ± 1 μM was calculated based on chemical shift perturbation of selected heme methyl resonances belonging to three different heme groups, caused by allosteric effects upon [Gd-DOTP](5-) binding to cytochrome c(3) at a molar ratio of 2. The other probe, [Gd-DOTAM](3+), caused PREs on a well-defined patch near the metal center of rubredoxin (especially the patch constituted by residues D19-G23 and W37-S45, which broaden beyond detection). This effect was partially reversed for some resonances (C6-Y11, in particular) when cytochrome c(3) was added to this system. Both probes were successful in causing reversible PREs at the partner binding site, thus showing to be good probes to identify partners' binding sites and since the interaction is reversible to structurally characterize protein complexes by better defining the complex interface.     

Evidence for strong tantalum-to-boron dative interactions in (silox)3Ta(BH3) and (silox)3Ta(eta2-B,Cl-BCl2Ph) (silox = tBu3SiO)1

Treatment of (silox)3Ta (1, silox = tBu3SiO) with BH3.THF and BCl2Ph afforded (silox)3Ta(BH3) (2) and (silox)3Ta(eta2-B,Cl-BCl2Ph) (3), which are both remarkably stable Ta(III) compounds. NMe3 and ethylene failed to remove BH3 from 2, and no indication of BH3 exchange with BH3.THF-d8 was noted via variable-temperature 1H NMR studies. Addition of BH3.THF to (silox)3TaH2 provided the borohydride-hydride (silox)3HTa(eta3-BH4) (5), and its thermolysis released H2 to generate 2. Exposure of 2 to D2 enabled the preparation of isotopologues (silox)3Ta(BH3-nDn) (n = 0, 2; 1, 2-D; 2, 2-D2; 3, 2-D3) for isotopic perturbation of chemical shift studies, but these failed to distinguish between "inverse adduct" (i.e., (silox)3Ta-->BH3) or (silox)3Ta(eta2-B,H-BH3) forms of 2. Computational models (RO)3Ta(BH3) (R = H, 2'; SiH3, 2SiH SiMe3, 2SiMe, and SitBu3, 2SiBu) were investigated to assess the relative importance of steric and electronic effects on structure and bonding. With small R, eta2-B,H structures were favored, but for 2SiMe and 2SiBu, the dative structure proved to be similar in energy. The electonic and vibrational features of both structure types were probed. The IR spectrum of 2 was best matched by the eta2-B,H conformer of 2SiBu. In related computations pertaining to 3, small R models favored the oxidative addition of a BCl bond, while with R = SitBu3 (3SiBu), an excellent match with its X-ray crystal structure revealed the critical steric influence of the silox ligands.     

A general approach toward bakkanes: short synthesis of (+/-)-bakkenolide-a (fukinanolide)

[reaction: see text] An efficient, general, and fully stereocontrolled approach to the family of bakkanes is disclosed. This route highlights a highly diastereoselective Diels-Alder/aldol sequence to furnish the common hydrindane precursor for the synthesis of bakkanes. The projected common intermediate was transformed to the (+/-)-bakkenolide-A in a short sequence.     

Sterically encumbered hexakis(alkylseleno)benzenes: conformational behavior of hexakis(iso-propylselenomethyl)benzene toward Hg ions on selective recognition

An efficient synthesis and structural aspects of a novel class of hexakis(alkylseleno)benzenes [(RSeCH₂)₆C₆] (R = Me, ⁱPr, ⁿBu, ^sBu, ^tBu, ⁿPn, ⁿHx, ⁿOct, 1-methylnaphthalene) by the reaction of hexakis(bromomethyl)benzene with RSe⁻ ions is demonstrated. Preliminary data on ion-sensing properties reveal that these species may act as selective ionophores for Hg²⁺ ions.     

Phosphoinositide-3-kinases (PI3Ks): combined comparative modeling and 3D-QSAR to rationalize the inhibition of p110alpha

The p110alpha isoform of the class IA PI3Ks was recently genetically validated as a promising target for anticancer therapy. However, up to now, only one compound (PIK75 = 1) has been reported as a very potent and selective inhibitor of this isoform. The lack of a 3D structure for this enzyme has clearly hindered the discovery of new p110alpha selective compounds. In view of this, we combined target-based (homology modeling) and ligand-based (3D-QSAR) approaches in an attempt to define an integrated interaction model for p110alpha inhibition. Twenty-five analogues of 1 were docked within the putative p110alpha binding site, and the molecular alignment generated was subsequently used to derive QSAR models based on scoring function, free energy of binding, CoMFA. and CoMSIA. The predictive power of these models was then analyzed using a challenging test set of 5 compounds. CoMSIA, and particularly CoMFA, models were found to outperform the other methods, predicting accurately the potency of 100% of the compounds in the test set, thereby validating our p110alpha homology model for use in further drug development.     

Strategies to stabilize new members of the (A3A'BO6)alpha (A3B3O0)beta homologous series in the Sr-Rh-O system: structure of the one-dimensional (alpha = 3, beta = 2) [Sr10(Sr0.5Rh1.5)TP(Rh6)Oh])24 oxide

The (alpha =3, beta =2) member of the (A3ABO6) (A3B3O9) homologous series has been stabilised in the Sr-Rh-O system for a [Sr10(Sr0.5Rh1.5)TP(Rh6)Oh]O24 composition. The structural characterisation has been performed by powder X-ray and electron diffraction measurements and high-resolution electron microscopy. In this structure, three face-sharing [RhO6] octahedra linked by one [Rh/SrO6] trigonal prism comprise the infinite one-dimensional chain that runs parallel to the c axis of a trigonal unit cell (Pc1), with parameters a=9.6411(1) and c=21.2440(4) A.     

Reactivity of cyclooligophosphanes: synthesis and structural characterisation of cyclo-1,4-(BH3)2(P4Ph4CH2) and cyclo-1,2-(BH3)2(P5Ph5)

The borane complexes cyclo-1,4-(BH3)2(P4Ph4CH2) (3) and cyclo-1,2-(BH3)2(P5Ph5) (4) were prepared by reaction of cyclo-(P4Ph4CH2) and cyclo-(P5Ph5) with BH3(SMe2). Only the 2:1 complexes 3 and 4 were isolated, even when an excess of the borane source was used. In solution, 3 exists as a mixture of the two diastereomers (R(P)*,S(P)*,S(P)*,R(P)*)-(+/-)-3 and (R(P)*,R(P)*,R(P)*,R(P)*)-(+/-)-3. However, in the solid state the (R(P)*,S(P)*,S(P)*,R(P)*)-(+/-) diastereomer is the major stereoisomer. Similarly, while only one isomer of 4 is observed in its X-ray structure, NMR spectroscopic investigations reveal that it forms a complex mixture of isomers in solution. 3 may be deprotonated with tBuLi to give the lithium salt cyclo-1,4-(BH3)2(P4Ph4CHLi) (3 x Li), though this could not be isolated in pure form.     

CMPO-functionalized C3-symmetric tripodal ligands in liquid/liquid extractions: efficient, selective recognition of Pu(IV) with low affinity for 3+ metal ions

Structural modifications of carbamoylmethylphosphine oxide (CPMO)-functionalized triphenoxymethane platforms are described, and the influence of these changes on the ability of the ligand to extract actinides from simulated acidic nuclear waste streams has been evaluated. The ligand system has been shown to have excellent binding efficiency and a selectivity for An(IV) in comparison to the a simple monomeric CMPO ligand under analogous conditions. Both the extraction efficiency and selectivity are strongly dependent on the flexibility and electronic properties of the ligating units in the triphenoxymethane construct. The Tb(III) and Bi(III) nitrate complexes of tris-CMPO derivatives have been isolated, and their structures were elucidated by NMR, ESI FT-ICR MS, and X-ray analysis, providing information on the interactions between metal ions and the tris-CMPO molecules.     

14-3-3 protein beta/alpha as a urinary biomarker for renal cell carcinoma: proteomic analysis of cyst fluid

Although various samples, including tissue, cells, serum, and urine, from patients with renal cell carcinoma (RCC) have been analyzed, biomarkers with diagnostic value have yet to be identified. We used a proteomics approach to analyze cyst fluid in cases of cyst-associated RCC to identify accessible and abundant proteins that are overexpressed and/or secreted by RCC cells. Proteins in the cyst fluid were separated by reverse-phase high-performance liquid chromatography and agarose two-dimensional gel electrophoresis and were identified by tandem mass spectrometry. We conducted a National Center for Biotechnology Information search and a MEDLINE search to predict the function of these identified proteins and to select a tumor-marker candidate protein. Our search resulted in the identification and selection of the differentially regulated protein known as 14-3-3 protein beta/alpha, which was overexpressed in cyst fluid from cyst-associated RCC but has not been previously associated with RCC. We then measured its incidence through Western blotting of various normal and RCC samples (serum, urine, tissue, and cyst fluid). The expression levels of 14-3-3 protein beta/alpha were higher in urine samples from patients with RCC than in samples from healthy volunteers. Receiver operating characteristic (ROC) curve analyses were performed to assess this potential biomarker; these data (area under the ROC curve value was 0.8813) indicate a high degree of accuracy for this screening method. 14-3-3 Protein beta/alpha may be a diagnostically useful biomarker for early diagnosis of RCC.     

Measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in (15)N,(13)C,(2)H-labeled proteins: application to domain orientation in maltose binding protein.

TROSY-based HN(CO)CA 2D and 3D pulse schemes are presented for measurement of (13)C(alpha)-(13)C(beta) dipolar couplings in high molecular weight (15)N,(13)C,(2)H-labeled proteins. In one approach, (13)C(alpha)-(13)C(beta) dipolar couplings are obtained directly from the time modulation of cross-peak intensities in a set of 2D (15)N-(1)HN correlated spectra recorded in both the presence and absence of aligning media. In a second approach 3D data sets are recorded with (13)C(alpha)-(13)C(beta) couplings encoded in a frequency dimension. The utility of the experiments is demonstrated with an application to an (15)N,(13)C,(2)H-labeled sample of the ligand free form of maltose binding protein. A comparison of experimental dipolar couplings with those predicted from the X-ray structure of the apo form of this two-domain protein establishes that the relative orientation of the domains in solution and in the crystal state are very similar. This is in contrast to the situation for maltose binding protein in complex with beta-cyclodextrin where the solution structure can be generated from the crystal state via a 11 degrees domain closure.     

Alpha-hydroxylation at C-15 and C-16 in cholesterol: synthesis of (25R)-5alpha-cholesta-3beta,15alpha,26-triol and (25R)-5alpha-cholesta-3beta,16alpha,26-triol from diosgenin

[reaction: see text] (25R)-5alpha-cholesta-3beta,16alpha,26-triol 7b and (25R)-5alpha-cholesta-3beta,15alpha,26-triol 10b were synthesized, via (25R)-5alpha-cholesta-3beta,16beta,26-triol 5a, from diosgenin 3 in 52% yield over six steps and 47% yield over eight steps, respectively. An efficient method for inversion of a C-16beta hydroxyl to the C-16alpha position and a short method for transposition of a C-16beta hydroxyl to the C-15alpha position via the unexpected beta-reduction of a C-15 ketone in a steroid are reported.     

Benzimidazole-5-sulfonamides as novel nonpeptide luteinizing hormone releasing hormone (LHRH) antagonists: minimization of mechanism-based CYP3A4 inhibition

Herein we report the development of novel, potent and non-peptide luteinizing hormone releasing hormone (LHRH) antagonists. The optimization towards derivatives free from mechanism-based CYP3A4 inhibition is described. The identification of a main metabolite guided us towards structural modifications of the benzyl moiety, which resulted in significant improvements of the CYP3A4 profile, while maintaining potent LHRH antagonist activity.     

Production of methyl-oxonium ion and its complexes in the core-excited (HC(O)OCH3)n clusters: H/H+ transfer from the alpha carbonyl

Dissociation of free methyl-formate (MF), HC(O)OCH3, and its clusters (MF)n, (HC(O)OCH3)n, induced by core-level excitation was studied near the oxygen K edge by time-of-flight fragment-mass spectroscopy. Besides the protonated clusters, (MF)nH+ with n < or = 15, we identified the production for another series of (MF)mCH3OH2+ with m < or = 14 as well as methyl-oxonium ion, CH3OH2+, characteristic of hydrogen transfer reactions in the cationic clusters. Here; specifically labeled methyl-formate-d (MFD), DC(O)OCH3 was also used to examine the core-excited dissociation mechanisms. Deuterium-labeled experiments indicated that MFD+ with low internal energies, partially generated after the core excitation, produces CH3OD+ via a site-specific deuterium transfer from the alpha carbonyl in the molecular cation and that CH3OD2+ can be formed via the successive transfer of another deuterium from the neighbor molecule in the clusters. The deuteron (proton) transfer was also found to take place preferentially from the alpha carbonyl of the neighbor molecule for the production of deuteronated (MFD)nD+, (protonated (MF)nH+), clusters. The minimal energy requirement paths were examined for dimer (MF)2+ cation to support the present dissociation mechanisms of core-excited (MF)n clusters using ab initio molecular-orbital calculations.     

Pt(II)-promoted [2 + 3] cycloaddition of azide to cyanopyridines: convenient tool toward heterometallic structures

The [2 + 3] cycloaddition reactions (which are greatly accelerated by microwave irradiation) of the di(azido)platinum(II) compounds cis-[Pt(N(3))(2)(PPh(3))(2)] (1) with cyanopyridines NCR (2) (R = 4-, 3-, and 2-NC(5)H(4)) give the corresponding bis(pyridyltetrazolato) complexes trans-[Pt(N(4)CR)(2)(PPh(3))(2)] (3) [R = 4-NC(5)H(4) (3a), 3-NC(5)H(4) (3b), and 2-NC(5)H(4) (3c)]. Compound 3c has been characterized as the N(1)N(2)-bonded isomer in the solid state by X-ray crystallography and represents the first bis(tetrazolato) complex of this kind. Complexes 3a and 3b have been used as metallaligands to generate heteronuclear coordination polymers in the presence of copper nitrate. A one-dimensional supramolecular architecture was obtained as the exclusive product, {trans-[Pt(2)(N(4)CR)(4)(PPh(3))(4)Cu](n)(NO(3))(2n).nH(2)O (4.nH(2)O) (R = 4-NC(5)H(4)), when 3a was employed, whereas with 3b the heteronuclear square complex trans-[Pt(N(4)CR)(2)(PPh(3))(2)Cu(NO(3))(2)(H(2)O)](2) (5) (R = 3-NC(5)H(4)), composed of Pt/Cu ions, was obtained. All the isolated complexes were characterized by IR, elemental, and (for 3b, 3c, 4, and 5) X-ray structural analyses. Complexes 3 were additionally characterized by (1)H, (13)C, and (31)P {(1)H} NMR spectroscopies.     

Prospects for the inhibition of the phosphatase domain of human soluble epoxide hydrolase (sEH-P)

Russian Chemical Bulletin - This brief review highlights the history of the discovery of the phosphatase domain of human soluble epoxide hydrolase (sEH-P). The data on its structure and...