Showing papers in "Molecular Diversity in 2004"

On reformulated Zagreb indices.

Abstract: Zagreb indices were reformulated in terms of the edge-degrees instead of the vertex-degrees as the original Zagreb indices. Three types of Zagreb indices were considered: original, modified and variable Zagreb indices. It is found that the optimum exponent of the variable reformulated Zagreb M 2 index (v=−1/2) is identical with the exponent of the vertex-connectivity index, which is the most used topological index in QSPR and QSAR. The close relationship between the graph and its line graph is used to relate the original and reformulated indices.

Profiling of generic anti-phosphopeptide antibodies and kinases with peptide microarrays using radioactive and fluorescence-based assays.

Abstract: Kinases represent one of the largest enzyme families and key regulatory proteins in the cell. Only a small subset of these enzymes has been characterised so far. We have prepared different types of phosphopeptide and peptide microarrays displaying peptides deduced from annotated human phosphorylation sites and cytoplasmic domains of all annotated human membrane proteins. This approach was enabled by fully-automated high throughput micro-scale synthesis of peptides by the SPOT technology combined with chemo-selective immobilisation on modified glass slides. The phosphopeptide microarrays displaying 2923 peptides in total have been used for the characterisation of commercially available generic anti-phosphopeptide antibodies. This enabled us to detect Abl kinase activity on a microarray with anti-phosphotyrosine antibodies yielding results comparable to those obtained from a radioactive assay. More than 13 000 peptides deposited on six glass slides were used to profile casein kinase 2 (CK2) using a radioactive assay, since no generic antibody for the reliable detection of serine or threonine phosphorylation could be identified. All previously identified substrates were detected in the microarray experiment. In order to confirm whether substrates on the microarray are substrates in solution phase assays, more than 700 peptides were synthesised and tested with CK2 in a solution phase assay. All substrates identified in the solution phase assay were also detected on the microarray.

High density peptide microarrays. In situ synthesis and applications

Abstract: The technologies enabling the creation of large scale, miniaturized peptide or protein microarrays are emerging. The focuses of this review are the synthesis and applications of peptide and peptidomimetic microarrays, especially the light directed parallel synthesis of individually addressable high density peptide microarrays using a novel photogenerated reagent chemistry and digital photolithography (Gao et al., 1998, J. Am. Chem. Soc. 120, 12698; Pellois et al. 2002, Nat. Biotechnol. 20, 922). Concepts related to the synthesis are discussed, such as the reactions of photogenerated acids in the deprotection step of peptide synthesis or oligonucleotide synthesis, and the applications of high density peptide chips in antibody binding assays are discussed. Peptide chips provide versatile tools for probing antigen-antibody, protein-protein, peptide-ligand interactions and are basic components for miniaturization, automation, and system integration in research and clinical diagnosis applications.

Cross-reactivity of T lymphocytes in infection and autoimmunity.

Abstract: T helper (Th) lymphocytes mediate critical effector and regulatory functions in infectious, allergic, or autoimmune diseases. Th cells possess clonal receptors that recognize antigenic peptides that are complexed with self-molecules of the major histocompatibility complex (MHC) on the surface of antigen presenting cells. An organism's repertoire of T cell receptors must be broad enough to recognize any possible microbial antigen. At the same time, tissue destruction resulting from the attack of autoreactive T lymphocytes that recognize self-peptides must be avoided. It was therefore believed that the immune system could distinguish between self and non-self antigens. This hypothesis was supported by several lines of evidence, including the seemingly exquisite specificity of immune responses. What, then, triggers autoaggressive attacks by the immune system? Clinical and epidemiological observations strongly suggest a link between infection and autoimmunity. A popular hypothesis considers autoimmunity as a side effect of antimicrobial immune responses. Cross-reactive T cells, capable of recognizing both microbial and self-peptides, have been prime suspects as instigators of autoimmunity ever since computerized data base searches revealed astonishing sequence homologies between microbial and self-peptides. Here we review recent data that show a previously unexpected degeneracy of antigen recognition by T cells. It has become clear that each individual T cell receptor can recognize a large number of different ligands. Furthermore, structural criteria rather than sequence homology dictate the antigen recognition process. Thus, the idea that cross-reactivity per se would cause autoimmune disease is most likely too simple. Instead, a variety of different molecular mechanisms dictate the immunological outcome of ligand recognition by T cells.

New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption, and Ames genotoxicity using topological descriptors

Abstract: In silico predictive models for aqueous solubility, human intestinal absorption (HIA), and Ames genotoxicity were developed principally using artificial neural net (ANN) analysis and topological descriptors. Approximately 10,000 compounds spread across three data sets were used in the construction of these quantitative-structure-activity/property-relationship (QSAR/QSPR) models. For aqueous solubility, 5,037 chemically diverse compounds were used to construct ANN-QSPRs for intrinsic aqueous solubility. When these robust models were applied to 938 compounds in external validation, they gave an r2= 0.78 with 84% predicted within 1 log unit for these new chemical entities (NCEs). 417 therapeutic drugs were used in the development of an ANN-QSPR to predict for percent oral absorption (%OA). For validation testing on 195 new drugs, 92% of the compounds were predicted to within 25% of their reported %OA values, which ranged from 0% to 100%. Polar surface area and logP, the octanol-water partition coefficient, were found to be important descriptors in our QSPR model. Development of an ANN-QSAR as a genotoxicity predictor for S. typhimurium employed 2963 compounds including 290 therapeutic drugs. Validation results on 400 NCEs with the ANN-QSAR gave a concordance of 83% which rose to 91% when a confidence indicator was applied. With new drugs a concordance of 92% was reached, which increased to 97% when the reliably indicator was invoked.

Peptide arrays with designed α-helical structures for characterization of proteins from FRET fingerprint patterns

Abstract: A practical high-throughput protein detection system is described, based on synthetic peptide arrays consisting of designed alpha-helical peptides, detected by fluorescence resonance energy transfer (FRET). Initially a model alpha-helical peptide known to interact with a structured protein, calmodulin, was selected to establish the strategy for high-throughput detection. In comparison to peptides with a single probe, a much higher FRET response has been observed with two fluorescent probes (7-diethylaminocoumarin-3-carboxylic acid and 5(6)-carboxy-fluorescein) at both termini of the synthetic peptides. To establish a reproducible high-throughput detection system, peptides were also immobilized onto a solid surface for detection of the target proteins. A small library of 112 different peptides was constructed, based on a model of the alpha-helical peptide with systematic replacement of residues carrying specific charges and/or hydrophobicities. The library was used to effectively characterize various proteins, giving their own 'protein fingerprint' patterns. The resulting 'protein fingerprints' correlate with the recognition properties of the proteins. The present microarray with designed synthetic peptides as the capturing agents is promising for the development of protein detection chips.

Creating molecular diversity from antioxidants in Brazilian propolis. Combination of TOPS-MODE QSAR and virtual structure generation.

Abstract: A QSAR model for antioxidative activity based on the Sub-Structural Molecular Design (TOPS-MODE) approach is developed for a series of compounds present in Brazilian propolis. This approach permitted the structural interpretation of the antioxidative activity of these compounds in terms of bond contributions. By these means we have identified the structural groups and regions that contribute to the antioxidative activity of the cinnamic acid and flavonoid derivatives present in the propolis. These results were then used to identify the positions and substituents to be used in a virtual compound generation experiment. Using this approach a total of 327 compounds were generated from which more than 70 are predicted to be more active than the most powerful antioxidants in the Brazilian propolis. From these 70 compounds less than 20 have been reported in the literature. Consequently, a high proportion of novel compounds with potential antioxidative activity has been identified by the current approach. This contributes to enhance the molecular diversity of the analogues of Brazilian propolis compounds with antioxidative properties.

Synthesis and dynamic NMR study of ketenimines derived from tert-butyl isocyanide, alkyl 2-arylamino-2-oxo-acetates, and dialkyl acetylenedicarboxylates

Abstract: The adduct produced in the reaction between tert-butyl isocyanide and dialkyl acetylenedicarboxylates was trapped by alkyl 2-arylamino-2-oxo-acetates. When the aryl group is 2-methyl-6-nitrophenyl or 2,6-di-isopropylphenyl, the product exists as two stable rotamers at room temperature as a result of restricted rotation around the Ar–N single bond. When the aryl group is 1-naphthyl or 8-quinolinyl, dynamic NMR effects are observed in the 1H NMR spectra. The calculated free-energy of activation for interconversion of the rotational isomers in 1-naphthyl and 8-quinolinyl derivatives amounts to about 99 ± 2 and 68.5 ± 2 kJ mol−1, respectively.

Development of small molecules that mimic the binding of ω-conotoxins at the N-type voltage-gated calcium channel

Abstract: Cone snails (Conidae) are marine predators with some extraordinary features. Their venom contains a hundred or more peptides that target numerous ion channels and receptors in mammals, including several that are involved in disease. ω-Conotoxins from fish hunting snails are 24–27 residue peptides with a rigid 4-loop cysteine framework that target the N-type voltage-gated calcium channel (VGCC). Two ω-conotoxins, MVIIA and CVID are currently in clinical development for chronic pain management (Ziconotide or Prialt, and AM336, respectively). In an attempt to develop small molecule equivalents of CVID, we defined the Cα–Cβ vectors of the residues believed to be important for binding to the N-type VGCC. Using these vectors, we undertook a virtual screening of virtual libraries approach to identify compounds that matched the pharmacophore. Cyclic pentapeptides containing residues of loop 2 of CVID, with one or more being a D-amino acid were designed and synthesised and were found to be active at the N-type VGCC (IC50∼ 20 μM). Agreeing with the specificity profile of CVID, molecules were inactive at the P/Q-type VGCC.

A reexamination of Biginelli-like multicomponent condensation reaction: One-pot regioselective synthesis of spiro heterobicyclic rings

Abstract: A pseudo four-component reaction is described, leading to the efficient regioselective synthesis of σ symmetric spiro heterobicyclic rings using aldehydes and urea in the presence of cyclic β-diester or β-diamides such as Meldrum's acid or barbituric acid derivatives. The reaction needs no added catalyst and proceeds solvent-free conditions at 80 °C.

A novel approach to chemical microarray using ketone-modified macromolecular scaffolds: Application in micro cell-adhesion assay

Abstract: This paper describes a novel strategy for the preparation of chemical microarrays using macro-molecular scaffolds. The macromolecular scaffolds are first functionalized with ketone groups and compounds of interest containing an aminooxy group are conjugated onto the ketone-modified scaffolds through a chemoselective oxime ligation. The conjugate mixtures are then spotted directly onto a plastic or glass surface to form compound microarrays. Because a constant amount of scaffold is used in the presence of excess compound in the ligation reaction, the amount of compound actually immobilized per microarray spot is constant and dependent on the scaffold concentration. Using this approach, 60 different peptides were ligated to human serum albumin or agarose scaffolds, and the peptide conjugates subsequently printed on glass or polystyrene surface to form microarrays. These peptide microarrays were subsequently evaluated and optimized for binding of Jurkat leukemic cancer cells.

New transport peptides broaden the horizon of applications for peptidic pharmaceuticals

Abstract: Protein transduction domains (PTDs) have proven to be an invaluable tool to transduce a wide variety of cargo's including peptides across the plasma membrane and into intact tissue. The PTDs are able to deliver biologically active molecules both in vitro and in vivo. This study describes many new polybasic PTDs of which some are just as potent as the PTDs derived from extracellular RNAses or other published PTDs. Large differences in potency became apparent when the PTDs are coupled to particular cargoes. Therefore, the unique characteristic of a PTD may only become apparent when it is selected for a particular application. Rules for optimization of PTDs for particular applications are now emerging and open the way for a new generation of drug delivery agents. Because fixation artifacts and irreversible membrane binding may cause misinterpretation of the amount of internalization of polybasic peptides, we have developed an enzyme transduction assay based on the intracellular loading of a cell permeable substrate. In this assay, a fluorescent signal is generated by internalized enzyme in intact cells and not by membrane-bound or extracellular enzyme.

QSAR study using topological indices for inhibition of carbonic anhydrase II by sulfanilamides and Schiff bases.

Abstract: A QSAR study of two sets of carbonic anhydrase inhibitors is presented using a variety of molecular descriptors including topological indices. The first set consists of 29 benzenesulphonamides, and the second set includes 35 sulphanilamide Schiff bases. Two regression methodologies have been used involving ridge regression and the CODESSA program, and their results are compared with those of previous QSAR studies. Good correlations were found for the former set, and less satisfactory results for the latter set when the number of molecular descriptors is kept below five.

Protein recognition using synthetic surface-targeted agents

Abstract: The design of synthetic agents to disrupt protein-protein interactions has received relatively little attention in recent years. In this review we describe strategies for targeting different types of protein surfaces using mimetics of protein secondary or tertiary structure. In this way strong and selective binding to a protein surface has be achieved and disruption of clinically important protein-protein interactions has been demonstrated in models of human disease.

Peptide transformation leading to peptide-peptidosulfonamide hybrids and oligo peptidosulfonamides.

Abstract: The sulfonamide moiety was introduced as a potential transition state isostere of the hydrolysis of the amide bond. Subsequently, the increased acidity of a sulfonamide N-H as compared to a regular amide N-H was explored in the development of peptidosulfonamide synthetic receptor molecules for binding and catalysis. The required building blocks for these compounds were accessible via an efficient synthesis, which also enabled the synthesis of oligopeptidosulfonamides as well as peptidosulfonamide-betapeptide hybrids. The structural consequences of the introduction of the peptidosulfonamide residues were studied and were further explored by the synthesis of cyclic peptidosulfonamides e.g. by ring-closing metathesis.

Mapping of a discontinuous and highly conformational binding site on follicle stimulating hormone subunit-β (FSH-β) using domain Scan™ and Matrix Scan™ technology

Abstract: This paper describes the application of two novel screening technologies, i.e. Domain Scan™ (24- and 30-mer peptides) and Matrix Scan™ (24-mer peptides)technology, in the mapping of a discontinuous epitope on FSH-β for a series of 20 monoclonal antibodies. 11 out of 20 mAb's, mapping of which was not successful by conventional Pepscan™ technology (12-merpeptides), showed selective binding to peptide-constructs corresponding to the β3-loop of FSH in the Domain™ and/or Matrix Scan™. Systematic replacement analysis studies with peptide-construct 57VYETVRVPGCAC-SAc-ADSLYTYPVATQ81 revealed that for most mAb's the amino acids R62, A70,D71, and L73 form the core of the epitope. A DomainScan™ performed in the C-O format showed highly selective binding for mAb's 1 and 2 with only three β1-β3 peptide-constructs covering the residues 60TVRVPGCAHHADSLY74 in combination with 10IAIEKEECRFAI21, while for mAb 10 binding was observed with peptide-constructs containing the C-terminal residues97RGLGPSYCSFGEMKE114 in combination with the residues 10IAIEKEECRFAI21. A Matrix Scan™ of mAb 17 showed that peptides from four different regions on FSH (1st strand β3-loop, α1-loop, longα2-loop, det. loop) showed enhanced binding in combination with several 70ADSL73-containing peptides. BIACORE measurements with mAb's 1, 2, 13, and 17 using a set of 21 different peptide(-construct)s partially confirmed the Domain and MatrixScan™ screening results. Only 24- and 33-mer peptides covering both the 1st and 2nd strand of the β3-loop showed measurable binding. Cyclic β3-loop peptide mimics were found to bind significantly stronger (Kd∼ 5 μM) than the lineair analogues, in agreement with the fact that the discontinuous epitope is part of a loop structure. Coupling of the lineair β1-peptide 10IAIEKEECRFAI21to the linear β3-peptide*52TFKELVYETVRVPGCAHHADSLYTYPVATQAH83# via disulfide bond formation showed a 2–3 fold increase in Kd, thus conforming participation of the β 1-loop in antibody binding for these mAb's.

Cellulose membrane supported peptide arrays for deciphering protein-protein interaction sites: The case of PIN, a protein with multiple natural partners

Abstract: Cellulose membrane supported peptide arrays, prepared according to the Spot method, allow the rapid identification and characterization of protein-protein interaction sites. Here, the method was used to screen reactive peptides from different proteins that bind to a single molecule, the PIN protein. PIN possesses two binding grooves, that have been shown to interact with several targets, including neuronal NO synthase, dynein intermediate chain, myosin V, the proapoptotic protein Bim, the scaffolding proteins DAP1α and gephyrin, and the transcription factor NRF-1. Arrays of peptides representing sequences of these targets were probed for reactivity with GST-tagged PIN, enabling the precise identification of binding motifs. Binding motifs were then minimized to seven or eight amino acid long peptides: YSKETQT for dynein IC, CDKSTQT for Bim, KDTGIQVD for nNOS, QSVGVQV for DAP1α and EDKNTMTD for myosin V. Alascan and substitution analysis provided proof that the Gln residue is critical for the interaction and cannot be easily replaced. Positions –1 and +1, just flanking the pivotal Gln, are also important; they consist of hydrophobic residues (Thr, Val) that could only be replaced by hydrophobic or aromatic amino acids. Position –4 is also critical for binding, with its Asp or Ser being replaceable to some extent. Alignment of sequences of proteins known to bind PIN shows that the most frequent amino acids in the motif are DKGTQT, consistent with the Spot results. We postulate that the degenerate character of binding to PIN is based on the propensity of several sequences to adopt a β-strand conformation that allows the Gln residue to position itself in the PIN channel and on the conformational breathing of the PIN binding groove.

The rational design of an anti-caries peptide against Streptococcus mutans.

Abstract: The cariogenic bacterium Streptococcus mutans attaches to tooth surfaces via a cell surface adhesin termed streptococcal antigen I/II (SA I/II). Mapping studies identified an adhesion epitope within residues 1025-1044. A synthetic peptide (p1025) spanning these residues inhibited adhesion of S. mutans in vitro and was tested in an in vivo human streptococcal adhesion model. Direct application of p1025 to the teeth prevented recolonisation of the oral cavity by S. mutans but not Actinomyces naeslundii. This review also describes various other adhesion-inhibiting peptides have been identified in vitro. We suggest that adhesion-blocking synthetic peptides may provide novel anti-infective agents. Topical application of such peptides at mucosal surfaces does not provide sustained selective pressure and in contrast to antibiotics, may not induce resistance.

Chemical synthesis of TASP arrays and their application in protein design

Abstract: A combinatorial synthesis of de novo proteins is described. The concept of template-assembled synthetic proteins (TASP) has been adapted to an orthogonal assembly of small libraries of purified peptide building blocks. It is combined with the spot synthesis of peptides which is exploited to array cyclic decapeptide templates on cellulose membranes. A cleavable linker on the cellulose allows control of the synthesis. The hydrophilic proteins are constructed by successive cleavage of orthogonal protecting groups on the template, followed by coupling of amphipathic helices in a predefined orientation and finally by incorporation of a cofactor. Libraries of peptides with variation of the amino acids expected to be close to the cofactor were coupled to the cellulose-bound template in all combinations, yielding up to 500 variants of a protein. Cofactors have been inserted either at non-covalent binding sites as heme and Cu2+ or by covalent modification of amino acids as Ru-bipyridine or flavin. The proteins were screened by recording their UV-vis spectra directly on the solid support. The properties screened include the redox potential of heme proteins, charge transfer bands indicating the ligation of Cu-centers, enzymatic activity, and folding stability. Synthesis of the best hits as soluble variants was used for detailed characterization. Iterative improvement in a second screening cycle was efficient in finding novel copper proteins. We discuss the prospects of synthesizing proteins by extending the concept to β-sandwich proteins and construction of efficient peptide libraries with computer-supported design, as well as the possible usage of improved solid phase materials.

Artificial neural networks: non-linear QSAR studies of HEPT derivatives as HIV-1 reverse transcriptase inhibitors.

Abstract: Structure-anti HIV activity relationships were established for a sample of 801-[2-hydroxyethoxy-methyl]-6-(phenylthio)thymine(HEPT) using a three-layer neural network (NN). Eight structural descriptors and physicochemical variables were used to characterize the HEPT derivatives under study. The network's architecture and parameters were optimized in order to obtain good results. All the NN architectures were able to establish a satisfactory relationship between the molecular descriptors and the anti-HIV activity. NN proved to give better results than other models in the literature. NN have been shown to be particularly successful in their ability to identify non-linear relationships.

Peptide antagonists of superantigen toxins.

Abstract: Superantigens produced by Staphylococcus aureus and Streptococcus pyogenes are among the most lethal of toxins. Toxins in this large family trigger an excessive cellular immune response leading to toxic shock. Superantigens are secreted by the bacteria as diverse natural mixtures, a complexity that demands development of broad-spectrum countermeasures. We used a rational approach to design short peptides with homology to various domains in a typical superantigen (staphylococcal enterotoxin B) and screened each peptide for its ability to antagonize, in human peripheral blood mononuclear cells, superantigen-mediated induction of the genes encoding T helper 1 cytokines that mediate shock: interleukin-2, interferon-gamma and tumor necrosis factor. A dodecamer peptide proved a potent antagonist against widely different superantigens. This peptide protected mice from killing by superantigens and it was able to rescue mice undergoing toxic shock. The antagonist peptide shows homology to a β-strand-hinge-α-helix domain that is structurally conserved among superantigens, yet currently of unknown function and remote from the binding sites for the known ligands essential for T cell activation, the major histocompatibility complex class II molecule and T cell receptor. The antagonist activity of this peptide thus identifies a novel domain in superantigens that is critical for their toxic action. The antagonist peptide provides a new tool for understanding the mechanism of excessive human immune response activation by superantigens that occurs during toxic shock and for identification of a novel target ligand that may interact with this superantigen domain.

QSPR modeling the aqueous solubility of alcohols by optimization of correlation weights of local graph invariants.

Abstract: Optimization of correlation weights of local graph invariants is an approach to model molecular properties and/or activities of chemical or/and biological interest. The essence of the approach may be described by means of three main steps: first, a descriptor which is a function of the weights of local graph invariants must be defined by the suitable choice among the different possibilities from the pool of molecular descriptors; second, correlation weights values which produce as large as possible correlation coefficient value between the selected property values and the descriptor data under consideration are calculated by Monte Carlo optimization procedure (the correlation coefficient is used as the quality objective function); third, a relationship such as property=C0+C1descriptor has to be calculated and validated with structures of some training set resorting to the standard least square method. We obtain quite satisfactory results using this calculation procedure to model the aqueous solubility of alcohols whose statistical characteristics are:n= 30, r= 0.9843, s= 0.176, F= 870 (Training Set);n= 33, r= 0.9965, s= 0.0902, F= 4456 (Test Set);n= 63, r= 0.9931, s= 0.121, F= 4379 (complete set of alcohol molecules).

Impact of different software implementations on the performance of the Maxmin method for diverse subset selection

Abstract: Besides the choice of an automated software method for selecting 'maximally diverse' compounds from a large pool of molecules, it is the implementation of the algorithm that critically determines the usefulness of the approach. The speed of execution of two implementations of the Maxmin algorithm is compared for the selection of maximally diverse subsets of large compound collections. Different versions of the software are compared using various C compiler options and Java virtual machines. The analysis shows that the Maxmin algorithm can be implemented in both languages yielding sufficient speed of execution. For large compound libraries the Java version outperformes the C version. While the Java version selects the same compounds independent of the virtual machine used, the C version produces slightly different subsets depending on the compiler and on the optimization settings.

New planar substrates for the in situ synthesis of peptide arrays.

Abstract: The performance of new cellulose membranes, aminofunctionalized via a PEG spacer, as a solid support in the synthesis of peptide arrays is described. The new membranes are stable to trifluoroacetic acid (TFA) and strong aqueous base for days. These properties extend the scope of synthesis considerably, e.g., more efficient side chain cleavage protocols can be applied which yielded peptides of improved purity. For the first time, cellulose membranes with a loading as high as 5 μmol/cm2 were accessible. Additionally, newly developed polypropylene membranes with hydroxy- or amino functionalities were successfully employed for the SPOT synthesis of peptides and phosphopeptides. The membranes are compatible with antibody binding as well as enzymatic phosphorylation assays.

Effective combinatorial strategy to increase affinity of carbohydrate binding by peptides.

Abstract: The Thomsen-Friedenreich antigen, a carcinoma-associated disaccharide involved in carcinoma cell homotypic aggregation and increased metastatic potential, has clinical value as a prognostic indicator and a marker of metastasized cells. Hence, it can reasonably be predicted that antigen-binding macromolecules are valuable clinical in vivo diagnostic/therapeutic targeting agents. Recently, we have selected first-generation antigen-binding peptides from a random peptide bacteriophage display library and have applied combinatorial affinity maturation to select functionally-maturated peptides, which target cultured carcinoma cells and inhibit carcinoma cell aggregation. In the current study we hypothesize that a targeted search of sequence space surrounding the antigen-binding consensus sequence will select unpredictable amino acid sequences in the non-consensus portions of the peptides, leading to increased affinity for the carbohydrate and greater solubility in physiological buffers. This comprehensive in vitro analysis demonstrates that preferential evolution of the amino-terminal sequence of the peptides occurred, which correlated, in structure/function studies, with the acquisition of maturated function. The maturated peptides are more soluble than the earlier peptides. Studies of peptide binding to the disaccharide indicate that two maturated peptides (P-30-1, F03) have higher affinity for the antigen and bind with higher intensity to the surface of cultured human carcinoma cells than the first-generation peptides. The results support our hypothesis that affinity maturation can improve carbohydrate binding by peptides and have theoretical importance as the first report of maturation of carbohydrate-binding affinity in a small, soluble peptide.

Counter-propagation artificial neural network as a tool for the independent variable selection: structure-mutagenicity study on aromatic amines.

Abstract: The counter-propagation artificial neural network (CP ANN) technique was applied for the independent variable selection and for structure-mutagenic potency modeling on a set of 95 aromatic and heteroaromatic amines with biological activity investigated experimentally by an in vitro assay. The molecular structures were represented by 275 independent variables classified as topostructural, topochemical, geometrical and quantum-chemical descriptors. As a result of the neural network modeling, the following descriptors were found to be the most important for structure-activity relationship:5χ -path connectivity index of order h= 5, 3χb C-bond cluster connectivity index of order h= 3, JB-Balaban's J index based on bond types, SHSNH2-electrotopological state index values for atoms, phia-flexibility index (κp1 ×κp2/nvx), IC 0-mean information content or complexity of a graph based on the 0 order neighborhood of vertices in a hydrogen-filled graph and ELUMO. The leave one out (LOO) method was used in order to test and select the models for mutagenicity prediction. The statistical parameters for the 7-descriptors model are R Model= 0.96 and R cv= 0.85, respectively. In the next step, the number of variables was reduced and the 4-descriptors model was found (R Model= 0.95 and R cv= 0.85) and classified as the best one.

Solution-phase reductive cyclization of 2-quinoxalinol analogs: systematic study of parallel synthesis.

Abstract: 1,5-Difluoro-2,4-dinitrobenzene starting material was treated via primary and/or secondary substitution with a variety of amino acids or amines and the aromatic m-dinitro groups were then reductively cyclized provide the 2-quinoxalinol analogs. The conditions for 1,5-dialkylamino-2,4-dinitrobenzene reduction have been systematically studied and optimized in solution. Three effective methods are described for the high-throughout generation of 2-quinoxalinol analogs.

Defining the antigenic structure of human GM-CSF and its implications for receptor interaction and therapeutic treatments

Abstract: Three epitopes of human Granulocyte-Macrophage Colony-Stimulating Factor (hGM-CSF) recognised by neutralising and non-neutralising monoclonal antibodies (mAbs) were characterised using competitive binding assays, dissociation constant measurements with glycosylated and non-glycosylated rhGM-CSF, bioactivity inhibition studies, and synthetic peptide arrays. Based on the first approach, two different binding sites were identified: an area referred to as A, recognised by mAbs M1B8 and CC5B5, and an area referred to as B, recognised by mAbs CC1H7 and CC3C12. These binding sites on hGM-CSF were accurately delineated using cytokine-derived overlapping peptide scans and combinatorial hexapeptide libraries prepared by SPOT synthesis on cellulose membranes. We assigned the identical linear epitope A1P2A3R4 to both non-neutralising mAbs CC1H7 and CC3C12. The conformational epitopes A18E21R23R24F119 and R23E21N17W13 recognised by mAb CC5B5, and P118F119EW13E14 recognised by mAb M1B8, were delineated by dual-positional scanning and subsequent iterative searches with two interrogating positions. Competitive binding assays with mAbs M1B8 and CC5B5 revealed the overlapping nature of the cytokine recognition. However, peptide library screening confirmed their binding to different epitopes of which the essential amino acids were found very closely located on the native protein surface. Inhibition of hGM-CSF biological activity by these mAbs demonstrated that these epitopes are located within or very near the receptor binding site of hGM-CSF. Finally, this work supports the importance of residues from helix A and residues from the C-terminal region of the cytokine, composing a common area that is indispensable for the cytokine's biological activity.

Chemolabile cellular microarrays for screening small molecules and peptides.

Abstract: Microarrays that mediate the uptake of small molecules into living cells are described. Tissue culture cells were seeded onto glass substrates functionalized locally with fluorescently labelled test substances. In order to enable a localized transfer of substances after contact of cells with the substrate, substances were immobilized on the surface either by non-covalent interactions or chemolabile linker groups. These chemolabile linker groups were incorporated into covalently immobilized compounds. Different ester linkages were evaluated as chemolabile linker groups. As model compounds, esters of the carboxy group of a cysteine with the hydroxy groups of carboxyfluorescein-labelled serine amide and tyrosine amide residues or the thiol group of another fluorescein-labelled cysteine amide were generated. Covalent immobilization occurred on maleimide-functionalized glass cover slips. The surface functionalization and release kinetics were assessed by confocal laser scanning microscopy. The fastest release was obtained for the phenolic tyrosine ester. Alternatively, fluorescently labelled peptides were immobilized by non-covalent interactions on glass and on a hydrogel matrix. In order to increase the efficiency of cellular uptake, peptides were N-terminally extended with a cell-penetrating peptide. Uptake of these peptides into cells was confined to the functionalized spots, and was specific for peptides extended with the cell-penetrating peptide.