Combinatorial enzymatic synthesis of heparan sulfate

Escherichia coli K5 heparosan was enzymatically modified by Chen and colleagues to construct a library of heparan sulfate polysaccharides for evaluation, leading to the discovery that a 2-O-sulfoiduronic acid residue is not essential for antithrombin-mediated anticoagulant activity in larger oligosaccharide and polysaccharide structures.     

Predicting sequences and structures of MHC-binding peptides: a computational combinatorial approach

Peptides bound to MHC molecules on the surface of cells convey critical information about the cellular milieu to immune system T cells. Predicting which peptides can bind an MHC molecule, and understanding their modes of binding, are important in order to design better diagnostic and therapeutic agents for infectious and autoimmune diseases. Due to the difficulty of obtaining sufficient experimental binding data for each human MHC molecule, computational modeling of MHC peptide-binding properties is necessary. This paper describes a computational combinatorial design approach to the prediction of peptides that bind an MHC molecule of known X-ray crystallographic or NMR-determined structure. The procedure uses chemical fragments as models for amino acid residues and produces a set of sequences for peptides predicted to bind in the MHC peptide-binding groove. The probabilities for specific amino acids occurring at each position of the peptide are calculated based on these sequences, and these probabilities show a good agreement with amino acid distributions derived from a MHC-binding peptide database. The method also enables prediction of the three-dimensional structure of MHC-peptide complexes. Docking, linking, and optimization procedures were performed with the XPLOR program [1].     

A novel approach to combinatorial library design

We address the problem of designing a general-purpose combinatorial library to screen for pharmaceutical leads. Conventional approaches focus on diversity as the primary factor in designing such libraries. We suggest making screening libraries out of a set of pharmaceutically relevant scaffolds, with multiple analogs per scaffold. The rationale for this rests on the fact that even though the hit-rate in active series is much higher than in the database as a whole, often a large fraction of the compounds in active series are inactive. This is especially true when the series has not been optimized for the target under study. We introduce the concept of hit-rate within a series and use historic screening data to arrive at a crude estimate for it. We then use simple probability arguments to show that 50-100 compounds are required in each series in order to be nearly certain of finding at least one active compound in each true active series for any given target.     

A combinatorial approach to branched polymers’ statistics

At least ideally, a certain class of polymers presents itself as a collection (set) of connected components. Each of these components is a cycle of trees, that is branched polymers eventually rooted on a cycle. We derive (and study) an equilibrium statistical model that accounts for the main connectivity features of such structures, whose origin is to be found in combinatorial probability. Phase transition (gel–soltransition) is shown to occur when some internal control parameter crosses one (critical parameter). Various structural asymptotic results are shown to be available using singularity analysis. This revised version was published online in July 2006 with corrections to the Cover Date.     

A combinatorial approach to the electron correlation problem

Starting from a path-integral formulation of quantum statistical mechanics expressed in a space of Slater determinants, we develop a method for the Monte Carlo evaluation of the energy of a correlated electronic system. The path-integral expression for the partition function is written as a contracted sum over graphs. A graph is a set of distinct connected determinants on which paths can be represented. The weight of a graph is given by the sum over exponentially large numbers of paths which visit the vertices of the graph. We show that these weights are analytically computable using combinatorial techniques, and they turn out to be sufficiently well behaved to allow stable Monte Carlo simulations in which graphs are stochastically sampled according to a Metropolis algorithm. In the present formulation, graphs of up to four vertices have been included. In a Hartree-Fock basis, this allows for paths which include up to sixfold excitations relative to the Hartree-Fock determinant. As an illustration, we have studied the dissociation curve of the N(2) molecule in a VDZ basis, which allows comparison with full configuration-interaction calculations.     

Using Raman spectroscopy to identify mixite minerals

Raman spectroscopy has been used to identify whether or not a selection of minerals labelled as mixites (formula BiCu6(AsO4)3(OH)6.3H2O) are correctly marked. Of the four samples, two samples are shown to be potentially mixites because of the presence of the characteristic Raman spectra of (AsO4)3- units and (HAsO4)- units, characterised by bands at around 803 and 833 cm(-1). Two of the minerals are shown to be predominantly carbonates. Bands are observed at 3473.9 and 3470.3 cm(-1) for the two mixite samples. Bands observed in the region 880-910 cm(-1) and in the 867-870 cm(-1) region are assigned to the AsO stretching vibrations of (HAsO4)2- and (H2AsO4)- units. Whilst bands at around 803 and 833 cm(-1) are assigned to the stretching vibrations of uncomplexed (AsO4)3- units. Intense bands observed at 473.7 and 475.4 cm(-1) are assigned to the nu4 bending mode of AsO4 units. Bands observed at around 386.5, 395.3 and 423.1 cm(-1) are assigned to the nu2 bending modes of the HAsO4 (434 and 400 cm(-1)) and the AsO4 groups (324 cm(-1)). Raman spectroscopy lends itself to the identification of minerals on host matrices and is especially useful for the identification of mixites.     

Template-directed approach to solid-phase combinatorial synthesis of furan-based libraries

A novel furan based scaffold 5-hydroxymethylfurfural has been identified for the generation of combinatorial libraries using template directed approach on solid phase. This scaffold has been utilized to afford furan-based bi-heterocyclic structures with extensive chemical diversity using cycloaddition, multicomponent and cyclization reactions.     

Catalytic enantioselective transamination of alpha-keto esters: an organic approach to enzymatic reactions

The half-transamination reaction of alpha-keto esters with pyridoxamine or 4-picolylamine was found to be catalysed by different metal catalysts in organic solvents giving moderate yields and enantioselectivities of up to 37% ee for methyl-3-indole pyruvate.     

HREELS to identify electronic structures of organic thin films

The electronic structure of alpha-oligothiophene (alphanT) thin films has been investigated for increasing chain lengths of n= 4-8 thiophene units with high resolution electron energy loss spectroscopy (HREELS) in the specular reflection geometry at a primary energy of 15 eV. The great advantage of this technique in contrast to UV/VIS absorption spectroscopy results from the fact, that the impact scattering mechanism of HREELS makes it possible to also detect optically forbidden electronic transitions. On the other hand, the electrons used as probes in HREELS have a wavelength which is two orders of magnitudes smaller if compared to those of photons used in UV/VIS absorption spectroscopy. Therefore individual molecules are excited by HREELS independent from each other and hence the excitation of collective excitons is not possible. As a result, information about the orientation of the molecules cannot be achieved with HREELS, which, however, is possible in polarization-dependent UV/VIS spectroscopy.     

HREELS to identify electronic structures of organic thin films

The electronic structure of -oligothiophene (nT) thin films has been investigated for increasing chain lengths of n=4–8 thiophene units with high resolution electron energy loss spectroscopy (HREELS) in the specular reflection geometry at a primary energy of 15 eV. The great advantage of this technique in contrast to UV/VIS absorption spectroscopy results from the fact, that the impact scattering mechanism of HREELS makes it possible to also detect optically forbidden electronic transitions. On the other hand, the electrons used as probes in HREELS have a wavelength which is two orders of magnitudes smaller if compared to those of photons used in UV/VIS absorption spectroscopy. Therefore individual molecules are excited by HREELS independent from each other and hence the excitation of collective excitons is not possible. As a result, information about the orientation of the molecules cannot be achieved with HREELS, which, however, is possible in polarization-dependent UV/VIS spectroscopy.     

A scalable approach to combinatorial library design for drug discovery

In this paper, we propose an algorithm for the design of lead generation libraries required in combinatorial drug discovery. This algorithm addresses simultaneously the two key criteria of diversity and representativeness of compounds in the resulting library and is computationally efficient when applied to a large class of lead generation design problems. At the same time, additional constraints on experimental resources are also incorporated in the framework presented in this paper. A computationally efficient scalable algorithm is developed, where the ability of the deterministic annealing algorithm to identify clusters is exploited to truncate computations over the entire data set to computations over individual clusters. An analysis of this algorithm quantifies the tradeoff between the error due to truncation and computational effort. Results applied on test data sets corroborate the analysis and show improvement by factors as large as 10 or more, depending on the data sets.     

Synthesis of the putative minimal FGF binding motif heparan sulfate trisaccharides by an orthogonal protecting group strategy

The synthesis of two trisaccharides, the putative minimal heparan sulfate sequences responsible for binding to acidic and basic fibroblast growth factors, respectively, is described from a common protected intermediate using an orthogonal protecting group strategy.     

Asymmetric synthesis of palitantin by an enzymatic and organocatalytic approach

The natural enantiomer of the fungal metabolite (+)-palitantin has been synthesized by adopting a chemoenzymatic and organocatalytic approach. Lipase catalyzed kinetic resolution, Sharpless asymmetric dihydroxylation and organocatalytic asymmetric hydroxymethylation are the key steps involved in the total synthesis of the target molecule.     

A global metabolite profiling approach to identify protein-metabolite interactions

Understanding the biochemical functions of proteins is an important factor in elucidating their cellular and physiological functions. Due to the predominance of biopolymer interactions in biology, many methods have been designed to interrogate and identify biologically relevant interactions that proteins make to DNA, RNA, and other proteins. Complementary approaches that can elucidate binding interactions between proteins and small molecule metabolites will impact the understanding of protein-metabolite interactions and fill a need that is outside the scope of current methods. Here, we demonstrate the ability to identify natural protein-metabolite interactions from complex metabolite mixtures by combining a protein-mediated small molecule enrichment step with a global metabolite profiling platform.     

A novel approach to tag and identify geranylgeranylated proteins

A recently developed proteomic strategy, the “GG‐azide”‐labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido‐geranylgeranyl analog and chemoselective derivatization of azido‐geranylgeranyl‐modified proteins by the “click” chemistry, using a tetramethylrhodamine‐alkyne. The resulting conjugated proteins can be separated by 1‐D or 2‐D and pH fractionation, and detected by fluorescence imaging. This method is compatible with downstream LC‐MS/MS analysis. Proteomic analysis of conjugated proteins by this approach identified several known geranylgeranylated proteins as well as Rap2c, a novel member of the Ras family. Furthermore, prenylation of progerin in mouse embryonic fibroblast cells was examined using this approach, demonstrating that this strategy can be used to study prenylation of specific proteins. The “GG‐azide”‐labeling approach provides a new tool for the detection and proteomic analysis of geranylgeranylated proteins, and it can readily be extended to other post‐translational modifications.     

The glomerular basement membrane as a model system to study the bioactivity of heparan sulfate glycosaminoglycans

The glomerular basement membrane and its associated cells are critical elements in the renal ultrafiltration process. Traditionally the anionic charge associated with several carbohydrate moieties in the glomerular basement membrane are thought to form a charge selective barrier that restricts the transmembrane flux of anionic proteins across the glomerular basement membrane into the urinary space. The charge selective function, along with the size selective component of the basement membrane, serves to limit the efflux of plasma proteins from the capillary lumen. Heparan sulfate glycosaminoglycans are anionically charged carbohydrate structures attached to proteoglycan core proteins and have a role in establishing the charge selective function of the glomerular basement membrane. Although there are a large number of studies in the literature that support this concept, the results of several recent studies using molecular genetic approaches to minimize the anionic charge of the glomerular basement membrane would suggest that the role of heparan sulfate glycosaminoglycans in the glomerular capillary wall are still not yet entirely resolved, suggesting that this research area still requires new and novel exploration.     

An enzymatic approach to the desymmetrization of disubstituted pyrrolines

The enzymatic desymmetrization of 2,2- and 2,5-disubstituted pyrroline compounds is reported in a procedure which gives access to both enantiomers in excellent enantiomeric excess and good yield. The enzyme reaction precursors are formed easily from two readily available substituted pyrroles using both ammonia (Na/NH3) and ammonia-free (Li/DBB) Birch reduction conditions.     

Quantitative chemical proteomics approach to identify post-translational modification-mediated protein-protein interactions

Post-translational modifications (PTMs) (e.g., acetylation, methylation, and phosphorylation) play crucial roles in regulating the diverse protein-protein interactions involved in essentially every cellular process. While significant progress has been made to detect PTMs, profiling protein-protein interactions mediated by these PTMs remains a challenge. Here, we report a method that combines a photo-cross-linking strategy with stable isotope labeling in cell culture (SILAC)-based quantitative mass spectrometry to identify PTM-dependent protein-protein interactions. To develop and apply this approach, we focused on trimethylated lysine-4 at the histone H3 N-terminus (H3K4Me(3)), a PTM linked to actively transcribed gene promoters. Our approach identified proteins previously known to recognize this modification and MORC3 as a new protein that binds H3M4Me(3). This study indicates that our cross-linking-assisted and SILAC-based protein identification (CLASPI) approach can be used to profile protein-protein interactions mediated by PTMs, such as lysine methylation.