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Natural products are a major source of biological molecules. The 3-methylfuran scaffold is found in a variety of plant secondary metabolite chemical elicitors that confer host-plant resistance against insect pests. Herein, the diversity-oriented synthesis of a natural-product-like library is reported, in which the 3-methylfuran core is fused in an angular attachment to six common natural product scaffolds-coumarin, chalcone, flavone, flavonol, isoflavone and isoquinolinone. The structural diversity of this library is assessed computationally using cheminformatic analysis. Phenotypic high-throughput screening of β-glucuronidase activity uncovers several hits. Further in vivo screening confirms that these hits can induce resistance in rice to nymphs of the brown planthopper Nilaparvata lugens. This work validates the combination of diversity-oriented synthesis and high-throughput screening of β-glucuronidase activity as a strategy for discovering new chemical elicitors. [ABSTRACT FROM AUTHOR]

A general and efficient Cu(II)-catalyzed cross-coupling method is reported for the preparation of acyclic tertiary amides. Generally moderate to excellent yields and functional group tolerance were obtained with secondary acyclic amides and aryl halides as substrates in toluene. [ABSTRACT FROM AUTHOR]

A systematic study of integrating statistical modeling and experimental analysis to investigate the cloud point (CP) and environmental risk of 82 structurally diverse nonionic surfactants is performed. During this procedure, the structural profiles of the studied compounds are characterized using hydrophilic domain and the whole molecular. Hundreds of descriptors, including constitutional, topological, geometrical, and electrostatic were calculated by the CODESSA program, and the resulting variables of the characterization selected by heuristic method are then modeled by the Gaussian process (GP). A variety of regression techniques, including MLR, PLS, SVM, and LSSVM are performed to a comprehensive comparison with GP on the basis of statistical analysis and experimental properties, in conjunction with the sophisticated variable selection methods, that is, empirical heuristic strategy. Among all the built models, the most predictable one is constructed based on the GP modeling combination of heuristic variable selection related to hydrophilic domain, with its predictive coefficient of determination ( ) and root-mean-square error of prediction (RMSP) on external independent test set of 0.962 and 5.200, respectively. The statistic model shows that the CP phenomenon is a comprehensive interaction of relative molecular weight, moments of inertia A, and topological structure account for hydrophilic part. [ABSTRACT FROM AUTHOR]

The L-proline-catalyzed oxidation of aliphatic primary alcohols with N-bromosuccimide (NBS) in water at room temperature to afford the corresponding dimeric esters in good to excellent yields was described. This pathway of dimeric esterification was proved to be very simple and environmentally friendly.[image omitted] [ABSTRACT FROM AUTHOR]

Sulfur atoms have been known to participate in hydrogen bonds (H-bonds) and these sulfur-containing H-bonds (SCHBs) are suggested to play important roles in certain biological processes. This study aims to comprehensively characterize all the SCHBs in 500 high-resolution protein structures (≤1.8 Å). We categorized SCHBs into six types according to donor/acceptor behaviors and used explicit hydrogen approach to distinguish SCHBs from those of nonhydrogen bonding interactions. It is revealed that sulfur atom is a very poor H-bond acceptor, but a moderately good H-bond donor. In α-helix, considerable SCHBs were found between the sulphydryl group of cysteine residue i and the carbonyl oxygen of residue i-4, and these SCHBs exert effects in stabilizing helices. Although for other SCHBs, they possess no specific secondary structural preference, their geometric characteristics in proteins and in free small compounds are significantly distinct, indicating the protein SCHBs are geometrically distorted. Interestingly, sulfur atom in the disulfide bond tends to form bifurcated H-bond whereas in cysteine-cysteine pairs prefer to form dual H-bond. These special H-bonds remarkably boost the interaction between H-bond donor and acceptor. By oxidation/reduction manner, the mutual transformation between the dual H-bonds and disulfide bonds for cysteine-cysteine pairs can accurately adjust the structural stability and biological function of proteins in different environments. Furthermore, few loose H-bonds were observed to form between the sulphydryl groups and aromatic rings, and in these cases the donor H is almost over against the rim rather than the center of the aromatic ring. Proteins 2009. © 2008 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

The organotin(IV) complexes of N-(2-mercaptophenyl)salicylaldimine,ROCOCH2CH2SnClL(L=OC6H4CH[dbnd]NC6H4S, R=alkyl), were synthesized by the reaction of 2-alkoxy carbonylethyltin trichlorides with N-(2-mercaptophenyl)salicylaldimine (H2L) in the presence of triethylamine and were characterized by elemental analyses, IR, 1H NMR spectra and X-ray single crystal diffraction. The structural features of these compounds are discussed. [ABSTRACT FROM AUTHOR]

Abstract: Quantitative structure–property relationships (QSPRs) on the basis of constitutional, topological, geometrical, and electrostatic descriptors are developed for 2454 13Cα NMR chemical shifts of 21 structure-known, high-quality monomeric proteins. In this procedure, heuristic approach is employed to perform variable-selection for obtaining few independent and significant descriptors. Coupled with various machine learning methods, including MLR, PLS, LSSVM, RF, and GP, these selected variables are then used to create both linear and nonlinear statistical models with the experimentally determined 13Cα NMR chemical shifts of proteins. In addition, the secondary structural effect and environmental influence on protein chemical shifts are also investigated in detail through structural survey and quantum-mechanical calculations. We demonstrate that (i) relationship between 13Cα NMR chemical shifts and local structural features is, to some extent, nonlinear, and (ii) the 13Cα chemical shift values are not only determined by corresponding side-chain conformations, but also affected from the arrangement and configuration of spatially vicinal residues. [Copyright &y& Elsevier]

Natural products are a major source of biological molecules. The 3-methylfuran scaffold is found in a variety of plant secondary metabolite chemical elicitors that confer host-plant resistance against insect pests. Herein, the diversity-oriented synthesis of a natural-product-like library is reported, in which the 3-methylfuran core is fused in an angular attachment to six common natural product scaffolds-coumarin, chalcone, flavone, flavonol, isoflavone and isoquinolinone. The structural diversity of this library is assessed computationally using cheminformatic analysis. Phenotypic high-throughput screening of β-glucuronidase activity uncovers several hits. Further in vivo screening confirms that these hits can induce resistance in rice to nymphs of the brown planthopper Nilaparvata lugens . This work validates the combination of diversity-oriented synthesis and high-throughput screening of β-glucuronidase activity as a strategy for discovering new chemical elicitors.

Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

Halide anions are traditionally recognized as the structure maker and breaker of bulk water to indirectly influence the physicochemical and biological properties of biomacromolecules immersed in electrolyte solution, but here we are more interested in whether they can be structured in the protein interior, forming that we named "halide motifs", to stabilize the protein architecture through direct noncovalent interactions with their context. In the current work, we present a systematical investigation on the energy components in 782 high-quality protein halide motifs retrieved from the Protein Data Bank (PDB), by means of the continuum electrostatic analysis coupled with nonelectrostatic considerations, as well as hybrid quantum mechanical/molecular mechanical (QM/MM) examination. We find that most halide motifs (91.6%) in our data set are substantially stabilizing, and their average stabilization energy is significantly larger than that previously obtained for sophisticated protein salt bridges (-15.16 vs -3.66 kcal/mol). Strikingly, nonelectrostatic factors, especially the dispersion potential, rather than the electrostatic aspect, dominate the energetic profile of the pronouncedly charged halide motifs, since the expensive cost for electrostatic desolvation penalty requires being paid off using the income receiving from the favorable Coulomb interactions during the motif formation. In addition, all the energy terms involved in halide motifs, regardless of their electrostatic or nonelectrostatic nature, highly depend on the degree of the motif's burial in the protein, and the buried halide motifs are generally associated with a high stability. The results presented herein should be of valuable use in establishing a knowledge framework toward understanding the functional implications underlying anion structured in a biological molecule.

Protein-DNA recognition plays a central role in the regulation of gene expression. With the rapidly increasing number of protein-DNA complex structures available at atomic resolution in recent years, a systematic, complete, and intuitive framework to clarify the intrinsic relationship between the global binding modes of these complexes is needed. In this work, we modified, extended, and applied previously defined RNA-recognition themes to describe protein-DNA recognition and used a protocol that incorporates automatic methods into manual inspection to plant a comprehensive classification tree for currently available high-quality protein-DNA structures. Further, a nonredundant (representative) data set consisting of 200 thematically diverse complexes was extracted from the leaves of the classification tree by using a locally sensitive interface comparison algorithm. On the basis of the representative data set, various physical and chemical properties associated with protein-DNA interactions were analyzed using empirical or semiempirical methods. We also examined the individual energetic components involved in protein-DNA interactions and highlighted the importance of conformational entropy, which has been almost completely ignored in previous studies of protein-DNA binding energy.

If considering that the pronouncedly charged halide anions are ubiquitous in the biological world, then it is interesting to ask whether the halogen-ionic bridges-this term is named by us to describe the interaction motif of a nonbonded halogen ion with two or more electrophiles simultaneously-commonly exist in biomolecules and how they contribute to the stability and specificity of biomolecular folding and binding? To address these problems, we herein present a particularly systematic investigation on the geometrical profile and the energy landscape of halogen ions interacting with and bridging between polar and charged molecular moieties in small model systems and real crystal structures, by means of ab initio calculation, database survey, continuum electrostatic analysis, and hybrid quantum mechanics/molecular mechanics examination. All of these unequivocally demonstrate that this putative halide motif is broadly distributed in biomolecular systems (>6000) and can confer a substantial stabilization for the architecture of proteins and their complexes with nucleic acids and small ligands. This stabilization energy is estimated to be generally more than 100 kcal·mol(-1) for gas-phase states or about 20 kcal·mol(-1) for solution conditions, which is much greater than that found in sophisticated water-mediated (<10 kcal·mol(-1)) and salt (∼ 3.66 kcal·mol(-1)) bridges. In this respect, we would expect that the proposed halogen-ionic bridge, which has long been unrecognized in the arena of biological repertoires, could be appreciated in chemistry and biology communities and might be exploited as a new and versatile tool for rational drug design and bioengineering.

A new method is described to measure the geometric similarity between protein-RNA interfaces quantitatively. The method is based on a procedure that dissects the interface geometry in terms of the spatial relationships between individual amino acid nucleotide pairs. Using this technique, we performed an all-on-all comparison of 586 protein-RNA interfaces deposited in the current Protein Data Bank, as the result, an interface-interface similarity score matrix was obtained. Based upon this matrix, hierarchical clustering was carried out which yielded a complete clustering tree for the 586 protein-RNA interfaces. By investigating the organizing behavior of the clustering tree and the SCOP classification of protein partners in complexes, a geometrically nonredundant, diverse data set (representative data set) consisting of 45 distinct protein-RNA interfaces was extracted for the purpose of studying protein-RNA interactions, RNA regulations, and drug design. We classified protein-RNA interfaces into three types. In type I, the families and interface structural classes of the protein partners, as well as the interface geometries are all similar. In type II, the interface geometries and the interface structural classes are similar, whereas the protein families are different. In type III, only the interface geometries are similar but the protein families and the interface structural classes are distinct. Furthermore, we also show two new RNA recognition themes derived from the representative data set., ((c) 2009 Wiley Periodicals, Inc.)

Although fluorination of pharmacologically active compounds has long been a common strategy to increase their metabolic stability and membrane permeation, the functionality of protein-ligand interactions involving fluorine atoms (fluorine bonding) was only recently recognized in the chemistry and biology communities. In this study, the geometric characteristics and the energetic behaviors of fluorine bonding were systematically investigated by combining two quite disparate but complementary approaches: X-ray structural analysis and theoretical calculations. We found that the short contacts involving fluorine atoms (generalized fluorine bonding) between proteins and fluorinated ligands are very frequent, and these contacts, compared to those routine hydrogen/halogen bonding, are more similar to sulfur-involved hydrogen bonding observed in proteins. ONIOM-based quantum mechanics/molecular mechanics analysis further revealed that fluorine bonding does play an essential role in protein-ligand binding, albeit the strength of isolated fluorine bonding is quite modest. Furthermore, 14 quantum mechanics (QM) and molecular mechanics (MM) methods were performed to reproduce fluorine bonding energies obtained at the rigorous MP2/aug-cc-pVDZ level of theory, and the results showed that most QM and very few MM methods perform well in the reproducibility; the MPWLYP functional and MMFF94 force field are recommended to study moderate and large fluorine bonding systems, respectively.