The glycan patterns at the individual glycosylation sites in orosomucoid from allergic reaction patients

Summary Little is known about the alterations that have occurred at the individual glycosylation sites in allergy patients or how these glycosylation patterns may change after anti-allergy treatments. Using reverse-phase HPLC, we have quantitated the glycoforms present at the individual glycosylation sites on orosomucoid isolated from the sera of allergic reaction patients and an allergic reaction patient treated with the antihistamine Terfenadine. The glycan structures isolated from the five glycosylation sites for the individual taking Terfenadine were all within normal ranges. It is suggested that if the changes in glycosylation in OMD in the allergic state are functionally driven, then it should be possible to correlate biological activities with quantitative changes at the individual glycosylation sites, and hence further define the role of OMD in allergy and inflammation.     

A Highly Efficient Glycosidation of Glycosyl Chlorides by Using Cooperative Silver(I) Oxide–Triflic Acid Catalysis

Following our discovery that silver(I) oxide-promoted glycosylation with glycosyl bromides can be greatly accelerated in the presence of catalytic TMSOTf or TfOH, we report herein a new discovery that glycosyl chlorides are even more effective glycosyl donors under these reaction conditions. The developed reaction conditions work well with a variety of glycosyl chlorides. Both benzoylated and benzylated chlorides have been successfully glycosidated, and these reaction conditions proved to be effective in coupling substrates containing nitrogen and sulfur atoms. Another convenient feature of this glycosylation is that the progress of the reaction can be monitored visually; its completion can be judged by the disappearance of the characteristic dark color of Ag₂O.     

Absolute Quantitation of Glycosylation Site Occupancy Using Isotopically Labeled Standards and LC-MS

N-linked glycans are required to maintain appropriate biological functions on proteins. Underglycosylation leads to many diseases in plants and animals; therefore, characterizing the extent of glycosylation on proteins is an important step in understanding, diagnosing, and treating diseases. To determine the glycosylation site occupancy, protein N-glycosidase F (PNGase F) is typically used to detach the glycan from the protein, during which the formerly glycosylated asparagine undergoes deamidation to become an aspartic acid. By comparing the abundance of the resulting peptide containing aspartic acid against the one containing non-glycosylated asparagine, the glycosylation site occupancy can be evaluated. However, this approach can give inaccurate results when spontaneous chemical deamidation of the non-glycosylated asparagine occurs. To overcome this limitation, we developed a new method to measure the glycosylation site occupancy that does not rely on converting glycosylated peptides to their deglycosylated forms. Specifically, the overall protein concentration and the non-glycosylated portion of the protein are quantified simultaneously by using heavy isotope-labeled internal standards coupled with LC-MS analysis, and the extent of site occupancy is accurately determined. The efficacy of the method was demonstrated by quantifying the occupancy of a glycosylation site on bovine fetuin. The developed method is the first work that measures the glycosylation site occupancy without using PNGase F, and it can be done in parallel with glycopeptide analysis because the glycan remains intact throughout the workflow.

Hydrogen bond activated glycosylation under mild conditions

Herein, we report a new glycosylation system for the highly efficient and stereoselective formation of glycosidic bonds using glycosyl N-phenyl trifluoroacetimidate (PTFAI) donors and a charged thiourea hydrogen-bond-donor catalyst. The glycosylation protocol features broad substrate scope, controllable stereoselectivity, good to excellent yields and exceptionally mild catalysis conditions. Benefitting from the mild reaction conditions, this new hydrogen bond-mediated glycosylation system in combination with a hydrogen bond-mediated aglycon delivery system provides a reliable method for the synthesis of challenging phenolic glycosides. In addition, a chemoselective glycosylation procedure was developed using different imidate donors (trichloroacetimidates, N-phenyl trifluoroacetimidates, N-4-nitrophenyl trifluoroacetimidates, benzoxazolyl imidates and 6-nitro-benzothiazolyl imidates) and it was applied for a trisaccharide synthesis through a novel one-pot single catalyst strategy.

A mild glycosylation system was developed using glycosyl imidate donors and a charge-enhanced thiourea H-bond donor catalyst. The method can be used for the effective synthesis of O-, C-, S- and N-glycosides and chemoselective one-pot glycosylation.     

Selective in vitro glycosylation of recombinant proteins: semi-synthesis of novel homogeneous glycoforms of human erythropoietin

BACKGROUND: A natural glycoprotein usually exists as a spectrum of glycosylated forms, where each protein molecule may be associated with an array of oligosaccharide structures. The overall range of glycoforms can have a variety of different biophysical and biochemical properties, although details of structure-function relationships are poorly understood, because of the microheterogeneity of biological samples. Hence, there is clearly a need for synthetic methods that give access to natural and unnatural homogeneously glycosylated proteins. The synthesis of novel glycoproteins through the selective reaction of glycosyl iodoacetamides with the thiol groups of cysteine residues, placed by site-directed mutagenesis at desired glycosylation sites has been developed. This provides a general method for the synthesis of homogeneously glycosylated proteins that carry saccharide side chains at natural or unnatural glycosylation sites. Here, we have shown that the approach can be applied to the glycoprotein hormone erythropoietin, an important therapeutic glycoprotein with three sites of N-glycosylation that are essential for in vivo biological activity. RESULTS: Wild-type recombinant erythropoietin and three mutants in which glycosylation site asparagine residues had been changed to cysteines (His(10)-WThEPO, His(10)-Asn24Cys, His(10)-Asn38Cys, His(10)-Asn83CyshEPO) were overexpressed and purified in yields of 13 mg l(-1) from Escherichia coli. Chemical glycosylation with glycosyl-beta-N-iodoacetamides could be monitored by electrospray MS. Both in the wild-type and in the mutant proteins, the potential side reaction of the other four cysteine residues (all involved in disulfide bonds) were not observed. Yield of glycosylation was generally about 50% and purification of glycosylated protein from non-glycosylated protein was readily carried out using lectin affinity chromatography. Dynamic light scattering analysis of the purified glycoproteins suggested that the glycoforms produced were monomeric and folded identically to the wild-type protein. CONCLUSIONS: Erythropoietin expressed in E. coli bearing specific Asn-->Cys mutations at natural glycosylation sites can be glycosylated using beta-N-glycosyl iodoacetamides even in the presence of two disulfide bonds. The findings provide the basis for further elaboration of the glycan structures and development of this general methodology for the synthesis of semi-synthetic glycoproteins.     

Molecularly imprinted polymers outperform lectin counterparts and enable more precise cancer diagnosis

Accurately analysing the particular glycosylation status of protein biomarkers is of significant importance in the precise, early diagnosis of cancer. Existing methods mainly rely on the use of antibodies and lectins. However, due to the macroscopic and microscopic heterogeneity of glycans, precise analysis of glycosylation status still remains a challenge. Molecularly imprinted polymers (MIPs), as a synthetic alternative to antibodies or lectins, may provide new solutions but have not yet been explored. Herein, we report an appealing strategy called triple MIP-based plasmonic immunosandwich assay (triMIP-PISA) for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers. As proof of the principle, alpha fetoprotein (AFP), which has been used as a clinical biomarker for early detection of hepatocellular carcinoma (HCC), as well as its Lens culinaris agglutinin (LCA)-reactive fraction (AFP-L3), which is mainly composed of core-fucosylated glycans, were used as two target proteoforms to test in this study. Using two MIPs that can specifically recognize the peptide sequence of AFP as well as a fucose-imprinted MIP that can specifically recognize the AFP-L3 fraction, facile simultaneous plasmon-enhanced Raman detection of AFP and AFP-L3 in serum was achieved, which allowed HCC patients to be distinguished from healthy individuals. Due to the excellent recognition properties of the MIPs that are comparable to those of antibodies and superior to those of lectins, our triMIP-PISA method exhibited improved precision as compared with an antibody plus lectin-based immunofluorescence assay. Thus, this strategy opened a new avenue towards the precise diagnosis of cancer.

A triple molecularly imprinted polymer (MIP)-based plasmonic assay was developed for precise cancer diagnosis in terms of the relative glycosylation expression of glycoprotein biomarkers.     

Energy saving and environment-friendly element-transfer reactions with industrial application potential

Herein we wish to propose the concept of "element-transfer reaction",which may afford the access to elemental compounds by transferring certain elements from easily available resources efficiently,concisely and precisely.A good element-transfer reaction with industrial application potential shall not generate waste and is performed under energy-saving and environment-friendly conditions.During the past decade,we have developed a series of methods for the synthesis of fluorine-and seleniumcontaining compounds via the fluorine-and selenium-transfer reactions,while the redox reactions we re considered to be the oxygen-and hydrogen-transfer reactions as well and were also widely studied by our group for producing the high-value-added fine chemicals.Some of these technologies have been successfully industrialized.This review summarizes our staged research results on fluorine-,oxygen-,hydrogen-and selenium-transfer reactions and makes a prospect on the developing trend in the field.     

唾液酸糖苷化反应研究新进展

唾液酸是一类重要的具有多种生物学功能的糖酸化合物. 唾液酸糖苷化反应条件较一般糖苷化反应苛刻, 立体选择性通常较差, 端基碳的立体构型较难控制. 在唾液酸糖苷化反应中能否高效地得到α糖苷键是评价该反应优劣的重要标志之一. 唾液酸苷化方法的研究一般涉及以下几个方面: C-2上的离去基团的运用, C-1, C-3上辅助基团的参与作用, C-5上氨基保护基团的修饰, 以及一些新的糖苷化反应催化剂的发展. 近些年来, 这些研究领域, 尤其是C-5上氨基保护基团的研究, 取得了重要进展. 将着重对唾液酸糖苷化方法的新进展做一总结和评述.     

Sugar-assisted glycopeptide ligation with complex oligosaccharides: scope and limitations

We have previously shown sugar-assisted ligation (SAL) to be a useful method for the convergent construction of glycopeptides. However to date SAL has only been carried out on systems where the thiol auxiliary is attached to a monosaccharide. For SAL to be truly applicable to the construction of fully elaborated glycopeptides and glycoproteins, it must be possible to carry out the reaction when the thiol auxiliary is attached to more elaborate sugars, as these are frequently what are observed in nature. Here we examine the effects of glycosylation at C-3, C-4, and C-6 of the C-2 auxiliary-containing glycan. Model glycopeptides where synthesized chemoenzymatically and reacted with peptide thioesters used in our previous work. These studies reveal that SAL is sensitive to extended glycosylation on the auxiliary-containing sugar. While it is possible to carry out SAL with extended glycosylation at C-4 and C-6, the presence of glycosylation at C-3 prevents the ligation from occurring. Additionally, with glycosylation at C-4 the ligation efficiency is affected by the identity of the N-terminal AA, while the nature of the C-terminal residue of the peptide thioester does not appear to affect ligation efficiency. These studies provide useful guidelines in deciding when it is appropriate to use SAL in the synthesis of complex glycopeptides and glycoproteins and how to choose ligation junctions for optimal yield.     

Mechanism of activation of a hafnium pyridyl-amide olefin polymerization catalyst: ligand modification by monomer

We have investigated the olefin polymerization mechanism of hafnium catalysts supported by a pyridyl-amide ligand with an ortho-metalated naphthyl group. Ethylene-alpha-olefin copolymers from these catalysts have broad molecular weight distributions that can be fit to a bimodal distribution. We propose a unique mechanism to explain this behavior involving monomer modification of the catalyst, which generates multiple catalyst species when multiple monomers are present. More specifically, we present evidence that the hafnium alkyl cation initially undergoes monomer insertion into the Hf-naphthyl bond, which permanently modifies the ligand to generate new highly active olefin polymerization catalysts. Under ethylene/octene copolymerization conditions, a plurality of new catalysts is formed in relative proportion to the respective monomer concentrations. Due to the asymmetry of the metal complex, two "ethylene-inserted" and eight "octene-inserted" isomers are possible, but it is a useful approximation to consider only one of each in the polymerization behavior. Consequently, gel permeation chromatography data for the polymers can be fit to a bimodal distribution having a continuous shift from a predominantly low molecular weight fraction to predominantly higher molecular weight fraction as [octene]/[ethylene] is increased. Theoretical calculations show that such insertions into the Hf-aryl bond have lower barriers than corresponding insertions into the Hf-alkyl bond. The driving forces for this insertion into the Hf-aryl bond include elimination of an eclipsing H-H interaction and formation of a stabilizing Hf-arene interaction. These new "monomer-inserted catalysts" have no beta-agostic interaction, very weak olefin binding, and olefin-insertion transition states which differ on the two sides by more than 4 kcal/mol. Thus, the barrier to site epimerization is very low and high polymerization rates are possible even when the chain wags prior to every insertion. Experimental evidence for aryl-insertion products is obtained from reactions of ethylene (13C2H4 NMR studies) or 4-methyl-1-pentene (4M1P) using relatively low monomer/catalyst ratios. Quantitative generation of monomer-inserted products is complicated by slow initiation kinetics followed by fast polymerization kinetics. However, NMR evidence for reaction with 13C2H4 was observed in situ at low temperature, and the attachment of monomer to ligand was confirmed by GC/MS and 13C NMR after quenching. Furthermore, a 4M1P-appended ligand was isolated from a polymerization reaction (50:1 monomer:catalyst) by column chromatography followed by multiple recrystallizations. One isomer was characterized by X-ray crystallography, which unequivocally shows a 4-methylpentyl substituent at the 2-position of the naphthyl, consistent with 1,2-insertion into the Hf-aryl bond. NMR suggests a second diastereomer (not isolated) is formed from a 1,2-insertion of opposite stereoselectivity.     

Mechanism of the catalytic action of semiconductors

Summary In conclusion, let us again ask ourselves the question formulated at the beginning of our paper; why does transfer of reaction from the gas phase to the surface of a semiconductor result in facilitation of the reaction? Answering this question is equivalent to answering the question of what the mechanism of the action of a semiconductor is.Investigation of the mechanism of chemisorption throws some light on this question. As we have seen, saturated molecules in passing into the chemisorbed state are converted into surface radicals. This in itself chemisorbed state are converted into surface radicals. This in itself increases their reactivity, for radicals are always more reactive than saturated molecules. Hence, the adsorption act itself, with which every heterogeneous catalytic process begins, results in increase in the reactivity of the molecules taking part in the process.In what then is the specific role of the catalyst?The transformation of molecules into surface radicals occurs, as we have seen, by the use of free valences of the surface itself. These surface valences therefore play the main part in the direction of the process. The catalyst is the carrier of such free valences. As we have seen, the functions of these free valences are performed by free electrons and holes in the crystal lattice.Hence, the crystal, taken as a whole, may be regarded as a sort of macroscopic molecule having unsaturated valences; it can be regarded as a sort of polyradical. The part played by free radicals in the kinetics of homogeneous reactions is well known. The introduction of such radicals into a medium in which reaction is occurring (i.e., the introduction of free valences) causes increase in reaction rate. In the case of catalysis, free valences are introduced by the catalyst itself. The introduction of these free valences stimulates the reaction. We arrive at the concept of the crystalline catalyst as a peculiar kind of polyradical. We must therefore abandon the long-held view of the existence of a difference in principle between heterogeneous catalysis and the kinetics of homogeneous reactions.Paper read at International Congress on Catalysis at Philadelphia, US, September 1956     

Reaction of nitric oxide at the beta-carbon of enamines. A new method of preparing compounds containing the diazeniumdiolate functional group

The reaction of nitric oxide (NO) with enamines has been investigated. Unlike previously reported reactions of NO as a free radical with alkenes, the electrophilic addition of NO to the beta-carbon of enamines results in the formation of compounds containing the diazeniumdiolate functional group (-[N(O)NO](-)). This reaction between NO and enamines has been shown to be quite general and a variety of enamine-derived diazeniumdiolates have been isolated and characterized. While enamines derived from aldehydes and ketones whose structures allow for sequential multiple electrophilic additions tended to undergo overreaction leading to unstable products, it has been shown that this complication may be overcome by suitable choice of reaction solvent. The products obtained may exist as zwitterionic iminium salts or as neutral species depending upon the structure of the parent enamine. The diazeniumdiolate derived from 1-(N-morpholino)cyclohexene is unique among the new compounds in that it spontaneously releases NO upon dissolution in buffered aqueous solution at pH 7.4 and 37 degrees C. While the total quantity of NO released by this material (ca. 7% of the theoretical 2 moles) is apparently limited by a competing reaction in which it hydrolyzes to an alpha-diazeniumdiolated carbonyl compound and the parent amine, this feature may prove to be of great value in the development of multiaction pharmaceuticals based upon this new type of NO-releasing compound. Reports of enzymatic (oxidative) release of NO from previously known carbon-bound diazeniumdiolates also suggest that analogues of these compounds may be useful as pharmaceutical agents. This new method of introducing the relatively rarely studied diazeniumdiolate functional group into organic compounds should lead to further research into its chemical and biological properties.     

Fine-tuning the spike: role of the nature and topology of the glycan shield in the structure and dynamics of the SARS-CoV-2 S

The dense glycan shield is an essential feature of the SARS-CoV-2 spike (S) architecture, key to immune evasion and to the activation of the prefusion conformation. Recent studies indicate that the occupancy and structures of the SARS-CoV-2 S glycans depend not only on the nature of the host cell, but also on the structural stability of the trimer; a point that raises important questions about the relative competence of different glycoforms. Moreover, the functional role of the glycan shield in the SARS-CoV-2 pathogenesis suggests that the evolution of the sites of glycosylation is potentially intertwined with the evolution of the protein sequence to affect optimal activity. Our results from multi-microsecond molecular dynamics simulations indicate that the type of glycosylation at N234, N165 and N343 greatly affects the stability of the receptor binding domain (RBD) open conformation, and thus its exposure and accessibility. Furthermore, our results suggest that the loss of glycosylation at N370, a newly acquired modification in the SARS-CoV-2 S glycan shield''s topology, may have contributed to increase the SARS-CoV-2 infectivity as we find that N-glycosylation at N370 stabilizes the closed RBD conformation by binding a specific cleft on the RBD surface. We discuss how the absence of the N370 glycan in the SARS-CoV-2 S frees the RBD glycan binding cleft, which becomes available to bind cell-surface glycans, and potentially increases host cell surface localization.

The N-glycans structures affect the mechanistic properties of the SARS-CoV-2 S, fine-tuning the glycoprotein. The evolution of the glycan shield led to the loss of N370 glycosylation in SARS-CoV-2 S, where the RBD cleft can bind host-cell glycans.     

The Callus of Phaseolus coccineus and Glycine max Biotransform Flavanones into the Corresponding Flavones

In vitro plant cultures are gaining in industrial importance, especially as biocatalysts and as sources of secondary metabolites used in pharmacy. The idea that guided us in our research was to evaluate the biocatalytic potential of newly obtained callus tissue towards flavonoid compounds. In this publication, we describe new ways of using callus cultures in the biotransformations. In the first method, the callus cultures grown on a solid medium are transferred to the water, the reaction medium into which the substrate is introduced. In the second method, biotransformation is carried out on a solid medium by growing callus cultures. In the course of the research, we have shown that the callus obtained from Phaseolus coccineus and Glycine max is capable of converting flavanone, 5-methoxyflavanone and 6-methoxyflavanone into the corresponding flavones.     

Glycosylation Profiling of Therapeutic Antibodies in Serum Samples Using a Microfluidic CD Platform and MALDI-MS

The serum clearance rate of therapeutic antibodies is important as it affects the clinical efficacy, required dose, and dose frequency. The glycosylation of antibodies has in some studies been shown to have an impact on the elimination rates in vivo. Monitoring changes to the glycan profiles in pharmacokinetics studies can reveal whether the clearance rates of the therapeutic antibodies depend on the different glycoforms, thereby providing useful information for improvement of the drugs. In this paper, a novel method for glycosylation analysis of therapeutic antibodies in serum samples is presented. A microfluidic compact-disc (CD) platform in combination with MALDI-MS was used to monitor changes to the glycosylation profiles of samples incubated in vitro. Antibodies were selectively purified from serum using immunoaffinity capture on immobilized target antigens. The glycans were enzymatically released, purified, and finally analyzed by MALDI-TOF-MS. To simulate changes to glycan profiles after administration in vivo, a therapeutic antibody was incubated in serum with the enzyme α1-2,3 mannosidase to artificially reduce the amount of the high mannose glycoforms. Glycan profiles were monitored at specific intervals during the incubation. The relative abundance of the high mannose 5 glycoform was clearly found to decrease and, simultaneously, that of high mannose 4 increased over the incubation period. The method can be performed in a rapid, parallel, and automated fashion for glycosylation profiling consuming low amounts of samples and reagents. This can contribute to less labor work and reduced cost of the studies of therapeutic antibodies glycosylation in vitro and in vivo.

Enzymatic removal of N‐glycans by PNGase F coated magnetic microparticles

Investigation of protein glycosylation is an important area in biomarker discovery and biopharmaceutical research. Alterations in protein N‐glycosylation can be an indication of changes in pathological conditions in the medical field or production parameters of biotherapeutics. Rapid development of these disciplines calls for fast, high‐throughput, and reproducible methods to analyze protein N‐glycosylation. Currently used methods require either long deglycosylation times or large excess of enzymes. In this paper, we report on the use of PNGase F immobilization onto the surface of magnetic microparticles and their use in rapid and efficient removal of N‐glycans from glycoproteins. The use of immobilized PNGase F also allowed reusability of the enzyme‐coated beads as the magnetic microparticles can be readily partitioned from the sample by a magnet after each deglycosylation reaction. The efficiency and activity of the PNGase F coated magnetic beads was compared with in‐solution enzyme reactions using standard glycoproteins possessing the major N‐glycan types of neutral, high mannose, and highly sialylated carbohydrates. The PNGase F coated magnetic beads offered comparable deglycosylation level to the conventional in‐solution based method in 10‐min reaction times for the model glycoproteins of immunoglobulin G (mostly neutral carbohydrates), ribonuclease B (high mannose type sugars), and fetuin (highly sialylated oligosaccharides) with the special features of easy removal of the enzyme from the reaction mixture and reusability.     

Synthesis and liquid crystalline properties of mono-, di- and tri-O-alkyl pentaerythritol derivatives bearing tri-, di- or monogalactosyl heads: the effects of curvature of molecular packing on mesophase formation

Self-organisation and self-assembly are critical to the stability of synthetic and biological membranes. Of particular importance is consideration of the packing arrangements of the various molecular species. Both phospho- and glycolipids can pack in ways in which curvature can be introduced into self-organised or self-assembled systems. For instance, it is known that the degree of curvature can affect the structures of any condensed phases that are formed. In this article we report on a systematic study in which we have varied the shapes of glycolipids and examined the condensed phases that they form. In doing so, we have also unified the shape dependency of lyotropic liquid crystals with those of thermotropic liquid crystals. In order to undertake this systematic study a range of different pentaerythritol derivatives was synthesized, which covers combinations of one to three alkyl chains of different lengths (6,7,9,10,11,12,14,16 carbon atoms) and three to one galactosyl heads. Mono- and di-O-galactosyl derivatives were prepared directly by glycosylation of the corresponding alcohols using 2,3,4,6-tetra-O-benzoyl or acetyl-alpha-D-galactopyranosyl trichloroacetimidate or bromide as the donors; the tri-O-galactosyl derivatives were synthesized from O-alkyl-O-benzyl di-O-galactosyl pentaerythritol intermediates, followed by de-O-benzylation and glycosylation steps. All of the fully deprotected products were obtained by standard methods, and their self-organising and self-assembling properties examined.     

ω-氨基酸缩聚反应动力学研究

前曾报导9-氨基壬酸的缩聚,从开始到反应程度p增加到99％左右时止,均遵循二级反应。在这以后,由于体系粘稠的影响,迅速转为三级反应。本文报导在6-氨基己酸和11-氨基十一酸缩聚时,也出现同样现象,即在p逐渐到高于99％左右时,反应从二级转变为三级。可以说这一现象是AB型单体聚酰胺化的一般规律,从而澄清了文献中对这一问题的不同论点。     

Using consensus-shape clustering to identify promiscuous ligands and protein targets and to choose the right query for shape-based virtual screening

Ligand-based shape matching approaches have become established as important and popular virtual screening (VS) techniques. However, despite their relative success, many authors have discussed how best to choose the initial query compounds and which of their conformations should be used. Furthermore, it is increasingly the case that pharmaceutical companies have multiple ligands for a given target and these may bind in different ways to the same pocket. Conversely, a given ligand can sometimes bind to multiple targets, and this is clearly of great importance when considering drug side-effects. We recently introduced the notion of spherical harmonic-based "consensus shapes" to help deal with these questions. Here, we apply a consensus shape clustering approach to the 40 protein-ligand targets in the DUD data set using PARASURF/PARAFIT. Results from clustering show that in some cases the ligands for a given target are split into two subgroups which could suggest they bind to different subsites of the same target. In other cases, our clustering approach sometimes groups together ligands from different targets, and this suggests that those ligands could bind to the same targets. Hence spherical harmonic-based clustering can rapidly give cross-docking information while avoiding the expense of performing all-against-all docking calculations. We also report on the effect of the query conformation on the performance of shape-based screening of the DUD data set and the potential gain in screening performance by using consensus shapes calculated in different ways. We provide details of our analysis of shape-based screening using both PARASURF/PARAFIT and ROCS, and we compare the results obtained with shape-based and conventional docking approaches using MSSH/SHEF and GOLD. The utility of each type of query is analyzed using commonly reported statistics such as enrichment factors (EF) and receiver-operator-characteristic (ROC) plots as well as other early performance metrics.     

New regioselective multicomponent reaction: one pot synthesis of spiro heterobicyclic aliphatic rings

In the context of our high-throughput organic synthesis program, we have studied the reactivity of special beta-keto esters toward the Biginelli reaction. We have found that a cyclic beta-keto ester reacts with one molecule of urea and two molecules of aldehyde to give a new family of spiro heterobicyclic aliphatic rings in good yields. Interestingly, the Biginelli product was not detected. After analysis of products using HPLC, 1H NMR, and 13C NMR, we have found that the reaction is driven by a regio-specific condensation of two molecules of aldehyde with the other reagents to afford only products harboring substituents exclusively in cis configuration. Monte Carlo minimization studies using MM2 force field suggest that cis products are energetically more stable than the trans counterparts. Together with previously reported data, these results suggest that the trans products were not obtained as result of steric hindrance produced by the equatorial position of one of the ring substituents. This new reaction is useful for high-throughput organic synthesis. Indeed, the new scaffold can be used to introduce additional groups in the molecules through remaining functional groups by a "domino strategy".