PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

PoSSuM (http://possum.cbrc.jp/PoSSuM/) is a database for detecting similar small-molecule binding sites on proteins. Since its initial release in 2011, PoSSuM has grown to provide information related to 49 million pairs of similar binding sites discovered among 5.5 million known and putative binding sites. This enlargement of the database is expected to enhance opportunities for biological and pharmaceutical applications, such as predictions of new functions and drug discovery. In this release, we have provided a new service named PoSSuM drug search (PoSSuMds) at http://possum.cbrc.jp/PoSSuM/drug_search/, in which we selected 194 approved drug compounds retrieved from ChEMBL, and detected their known binding pockets and pockets that are similar to them. Users can access and download all of the search results via a new web interface, which is useful for finding ligand analogs as well as potential target proteins. Furthermore, PoSSuMds enables users to explore the binding pocket universe within PoSSuM. Additionally, we have improved the web interface with new functions, including sortable tables and a viewer for visualizing and downloading superimposed pockets.

Enantioselective Direct Alkynylation of Ketones Catalyzed by Chiral CCN Pincer RhIII Complexes.

A direct asymmetric alkynylation of ketones with new chiral CCN Rh catalysts containing N-heterocyclic carbene and oxazoline hybrid ligands is described. The catalytic reaction of fluoroalkyl-substituted ketones, ArCOCF2 X (X=F, Cl, H), with aromatic and aliphatic alkynes yielded the corresponding chiral propargyl alcohols with high enantioselectivity. Control and kinetic experiments suggested a bis(alkynyl) Rh intermediate as the active species for the C-C bond-forming step.

Asymmetric Three-Component Coupling Reaction of Alkyne, Enone, and Aldehyde Catalyzed by Chiral Phebox Ruthenium Catalysts.

Catalytic asymmetric three-component coupling reactions of terminal alkynes, α,ß-unsaturated ketones, and aldehydes were studied. The chiral ruthenium complexes containing bis(oxazolinyl)phenyl ligands were found to serve as efficient catalysts for a tandem reaction based on conjugate addition of terminal alkynes to α,ß-unsaturated ketones and subsequent aldol reaction with aldehydes, giving ß-hydroxyketone derivatives containing α-propargyl groups in high yields with moderate to good enantioselectivities. This method can produce various functional molecules from commercially available substrates in a one-pot procedure. The absolute configuration of the major product was determined by X-ray analysis. The control experiments suggested that a ruthenium enolate species generated in situ by conjugate addition could be involved as an intermediate for the aldol coupling with an aldehyde.

Asymmetric Induction at Remote Quaternary Centers of Cyclohexadienones by Rhodium-Catalyzed Conjugate Hydrosilylation.

The enantioselective desymmetrizing conjugate hydrosilylation of prochiral differently γ,γ-disubstituted cyclohexadienone derivatives 2 to furnish the corresponding cyclohexenones 4 with a remote chiral all-carbon quaternary center at the γ position is described. Chiral rhodium-bis(oxazolinyl)phenyl complexes 1 were effective catalysts for this transformation. This catalytic system was extended to the asymmetric transformation of spirocarbocyclic cyclohexadienones 5 to give the corresponding products 6 with high enantiomeric ratios.

Co6 H8 (Pi Pr3 )6 : A Cobalt Octahedron with Face-Capping Hydrides.

A square-planar Co4 amide cluster, Co4 {N(SiMe3 )2 }4 (2), and an octahedral Co6 hydride cluster, Co6 H8 (Pi Pr3 )6 (4), were obtained from metathesis-type amide to hydride exchange reactions of a CoII amide complex with pinacolborane (HBpin) in the absence/presence of Pi Pr3 . The crystal structure of 4 revealed face-capping hydrides on each triangular [Co3 ] face, while the formal CoII2 CoI4 oxidation state of 4 indicated a reduction of the cobalt centers during the assembly process. Cluster 4 catalyzes the hydrosilylation of 2-cyclohexen-1-one favoring the conjugate reduction. Generation of the catalytically reactive Co cluster species was indicated by a trapping experiment with a chiral chelating agent.

PoSSuM: a database of similar protein-ligand binding and putative pockets.

Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ~33,000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/.

Room temperature dehydrogenation of ethane, propane, linear alkanes C4-C8, and some cyclic alkanes by titanium-carbon multiple bonds.

The transient titanium neopentylidyne, [(PNP)Ti≡C(t)Bu] (A; PNP(-)≡N[2-P(i)Pr2-4-methylphenyl]2(-)), dehydrogenates ethane to ethylene at room temperature over 24 h, by sequential 1,2-CH bond addition and ß-hydrogen abstraction to afford [(PNP)Ti(η(2)-H2C═CH2)(CH2(t)Bu)] (1). Intermediate A can also dehydrogenate propane to propene, albeit not cleanly, as well as linear and volatile alkanes C4-C6 to form isolable α-olefin complexes of the type, [(PNP)Ti(η(2)-H2C═CHR)(CH2(t)Bu)] (R = CH3 (2), CH2CH3 (3), (n)Pr (4), and (n)Bu (5)). Complexes 1-5 can be independently prepared from [(PNP)Ti═CH(t)Bu(OTf)] and the corresponding alkylating reagents, LiCH2CHR (R = H, CH3(unstable), CH2CH3, (n)Pr, and (n)Bu). Olefin complexes 1 and 3-5 have all been characterized by a diverse array of multinuclear NMR spectroscopic experiments including (1)H-(31)P HOESY, and in the case of the α-olefin adducts 2-5, formation of mixtures of two diastereomers (each with their corresponding pair of enantiomers) has been unequivocally established. The latter has been spectroscopically elucidated by NMR via C-H coupled and decoupled (1)H-(13)C multiplicity edited gHSQC, (1)H-(31)P HMBC, and dqfCOSY experiments. Heavier linear alkanes (C7 and C8) are also dehydrogenated by A to form [(PNP)Ti(η(2)-H2C═CH(n)Pentyl)(CH2(t)Bu)] (6) and [(PNP)Ti(η(2)-H2C═CH(n)Hexyl)(CH2(t)Bu)] (7), respectively, but these species are unstable but can exchange with ethylene (1 atm) to form 1 and the free α-olefin. Complex 1 exchanges with D2C═CD2 with concomitant release of H2C═CH2. In addition, deuterium incorporation is observed in the neopentyl ligand as a result of this process. Cyclohexane and methylcyclohexane can be also dehydrogenated by transient A, and in the case of cyclohexane, ethylene (1 atm) can trap the [(PNP)Ti(CH2(t)Bu)] fragment to form 1. Dehydrogenation of the alkane is not rate-determining since pentane and pentane-d12 can be dehydrogenated to 4 and 4-d12 with comparable rates (KIE = 1.1(0) at ~29 °C). Computational studies have been applied to understand the formation and bonding pattern of the olefin complexes. Steric repulsion was shown to play an important role in determining the relative stability of several olefin adducts and their conformers. The olefin in 1 can be liberated by use of N2O, organic azides (N3R; R = 1-adamantyl or SiMe3), ketones (O═CPh2; 2 equiv) and the diazoalkane, N2CHtolyl2. For complexes 3-7, oxidation with N2O also liberates the α-olefin.

Rice slender leaf 1 gene encodes cellulose synthase-like D4 and is specifically expressed in M-phase cells to regulate cell proliferation.

Cellulose synthase-like (CSL) genes are predicted to catalyse the biosynthesis of non-cellulosic polysaccharides such as the ß-D-glycan backbone of hemicelluloses and are classified into nine subfamilies (CSLA-CSLH and CSLJ). The CSLD subfamily is conserved in all land plants, and among the nine CSL subfamilies, it shows the highest sequence similarity to the cellulose synthase genes, suggesting that it plays fundamental roles in plant development. This study presents a detailed analysis of slender leaf 1 (sle1) mutants of rice that showed rolled and narrow leaf blades and a reduction in plant height. The narrow leaf blade of sle1 was caused by reduced cell proliferation beginning at the P3 primordial stage. In addition to the size reduction of organs, sle1 mutants exhibited serious developmental defects in pollen formation, anther dehiscence, stomata formation, and cell arrangement in various tissues. Map-based cloning revealed that SLE1 encodes the OsCSLD4 protein, which was identified previously from a narrow leaf and dwarf 1 mutant. In situ hybridization experiments showed that OsCSLD4 was expressed in a patchy pattern in developing organs. Double-target in situ hybridization and quantitative RT-PCR analyses revealed that SLE1 was expressed specifically during the M-phase of the cell cycle, and suggested that the cell-cycle regulation was altered in sle1 mutants. These results suggest that the OsCSLD4 protein plays a pivotal role in the M phase to regulate cell proliferation. Further study of OsCSLD4 is expected to yield new insight into the role of hemicelluloses in plant development.

Direct conjugate addition of alkynes with α,ß-unsaturated carbonyl compounds catalyzed by NCN-pincer Ru complexes.

NCN-pincer Ru-complexes containing bis(oxazolinyl)phenyl ligands serve as suitable catalysts in the direct conjugate additions of α,ß-unsaturated carbonyl compounds, including ketones, esters, and amides, as well as vinylphosphonates, giving various ß-alkynyl carbonyl and phosphonate compounds. A bis(oxazolinyl)phenyl (phebox)-Ru complex also catalyzes the asymmetric conjugate addition of an alkyne with a ß-substituted, α,ß-unsaturated ketone to produce a chiral ß-alkynyl ketone.

PDB-scale analysis of known and putative ligand-binding sites with structural sketches.

Computational investigation of protein functions is one of the most urgent and demanding tasks in the field of structural bioinformatics. Exhaustive pairwise comparison of known and putative ligand-binding sites, across protein families and folds, is essential in elucidating the biological functions and evolutionary relationships of proteins. Given the vast amounts of data available now, existing 3D structural comparison methods are not adequate due to their computation time complexity. In this article, we propose a new bit string representation of binding sites called structural sketches, which is obtained by random projections of triplet descriptors. It allows us to use ultra-fast all-pair similarity search methods for strings with strictly controlled error rates. Exhaustive comparison of 1.2 million known and putative binding sites finished in ∼30 h on a single core to yield 88 million similar binding site pairs. Careful investigation of 3.5 million pairs verified by TM-align revealed several notable analogous sites across distinct protein families or folds. In particular, we succeeded in finding highly plausible functions of several pockets via strong structural analogies. These results indicate that our method is a promising tool for functional annotation of binding sites derived from structural genomics projects.

A DYNC1H1 mutation causes a dominant spinal muscular atrophy with lower extremity predominance.

Whole-exome sequencing of two affected sibs and their mother who showed a unique quadriceps-dominant form of neurogenic muscular atrophy disclosed a heterozygous DYNC1H1 mutation [p.H306R (c.917A>G)]. The identical mutation was recently reported in a pedigree with the axonal form of Charcot-Marie-Tooth disease. Three other missense mutations in DYNC1H1 were also identified in families with dominant spinal muscular atrophy with lower extremity predominance. Their clinical features were consistent with those of our family. Our study has demonstrated that the same DYNC1H1 mutation could cause spinal muscular atrophy as well as distal neuropathy, indicating pleotropic effects of the mutation.

Enantioselective synthesis of optically active 3,3-diarylpropanoates by conjugate hydrosilylation with chiral Rh-bis(oxazolinyl)phenyl catalysts.

Conjugate hydrosilylation of 3,3-diarylacrylate derivatives catalyzed by chiral rhodium-bis(oxazolinyl)phenyl complexes (1 mol %) at 60 °C for 2 h was investigated to prepare optically active 3,3-diarylpropanoate derivatives in high yields up to 99% yield and high enantioselectivities up to 99%.

Cooperative catalytic activation of Si-H bonds by a polar Ru-S bond: regioselective low-temperature C-H silylation of indoles under neutral conditions by a Friedel-Crafts mechanism.

Merging cooperative Si-H bond activation and electrophilic aromatic substitution paves the way for C-3-selective indole C-H functionalization under electronic and not conventional steric control. The Si-H bond is heterolytically split by the Ru-S bond of a coordinatively unsaturated cationic ruthenium(II) complex, forming a sulfur-stabilized silicon electrophile. The Wheland intermediate of the subsequent Friedel-Crafts-type process is assumed to be deprotonated by the sulfur atom, no added base required. The overall catalysis proceeds without solvent at low temperature, only liberating dihydrogen.

Iron- and cobalt-catalyzed asymmetric hydrosilylation of ketones and enones with bis(oxazolinylphenyl)amine ligands.

Chiral bis(oxazolinylphenyl)amines proved to be efficient auxiliary ligands for iron and cobalt catalysts with high activity for asymmetric hydrosilylation of ketones and asymmetric conjugate hydrosilylation of enones.

Universal partitioning of the hierarchical fold network of 50-residue segments in proteins.

BACKGROUND: Several studies have demonstrated that protein fold space is structured hierarchically and that power-law statistics are satisfied in relation between the numbers of protein families and protein folds (or superfamilies). We examined the internal structure and statistics in the fold space of 50 amino-acid residue segments taken from various protein folds. We used inter-residue contact patterns to measure the tertiary structural similarity among segments. Using this similarity measure, the segments were classified into a number (Kc) of clusters. We examined various Kc values for the clustering. The special resolution to differentiate the segment tertiary structures increases with increasing Kc. Furthermore, we constructed networks by linking structurally similar clusters. RESULTS: The network was partitioned persistently into four regions for Kc >or= 1000. This main partitioning is consistent with results of earlier studies, where similar partitioning was reported in classifying protein domain structures. Furthermore, the network was partitioned naturally into several dozens of sub-networks (i.e., communities). Therefore, intra-sub-network clusters were mutually connected with numerous links, although inter-sub-network ones were rarely done with few links. For Kc >or= 1000, the major sub-networks were about 40; the contents of the major sub-networks were conserved. This sub-partitioning is a novel finding, suggesting that the network is structured hierarchically: Segments construct a cluster, clusters form a sub-network, and sub-networks constitute a region. Additionally, the network was characterized by non-power-law statistics, which is also a novel finding. CONCLUSION: Main findings are: (1) The universe of 50 residue segments found here was characterized by non-power-law statistics. Therefore, the universe differs from those ever reported for the protein domains. (2) The 50-residue segments were partitioned persistently and universally into some dozens (ca. 40) of major sub-networks, irrespective of the number of clusters. (3) These major sub-networks encompassed 90% of all segments. Consequently, the protein tertiary structure is constructed using the dozens of elements (sub-networks).

Modulation of the coordination geometries of NCN and NCNC Rh complexes for ambidextrous chiral catalysts.

A chirality switch between novel NCN pincer Rh complexes and a related double cyclometalated NCNC Rh complex containing secondary amino groups is described. Their catalytic abilities were determined in asymmetric alkynylation of ethyl trifluoropyruvate, and the change in the coordination geometry of the Rh catalysts affected the stereochemistry of the products.

A new NCN pincer ruthenium complex and its catalytic activity for enantioselective hydrogenation of ketones.

New bis(oxazolinyl)phenyl-ruthenium(II) complexes, which were synthesized by C-H bond activation with RuCl(3).3H(2)O in zinc powder and 1,5-cyclooctadine followed by ligand exchange reaction with sodium acetylacetonate or acetylacetone, exhibited enantioselective hydrogenation of ketones in up to 90% ee.

Simulation study on the disordered state of an Alzheimer's beta amyloid peptide Abeta(12 36) in water consisting of random-structural, beta-structural, and helical clusters.

The monomeric Alzheimer's beta amyloid peptide, Abeta, is known to adopt a disordered state in water at room temperature, and a circular dichroism (CD) spectroscopy experiment has provided the secondary-structure contents for the disordered state: 70% random, 25% beta-structural, and 5% helical. We performed an enhanced conformational sampling (multicanonical molecular dynamics simulation) of a 25-residue segment (residues 12-36) of Abeta in explicit water and obtained the conformational ensemble over a wide temperature range. The secondary-structure contents calculated from the conformational ensemble at 300 degrees K reproduced the experimental secondary-structure contents. The constructed free-energy landscape at 300 degrees K was not plain but rugged with five clearly distinguishable clusters, and each cluster had its own characteristic tertiary structure: a helix-structural cluster, two beta-structural clusters, and two random-structural clusters. This indicates that the contribution from the five individual clusters determines the secondary-structure contents experimentally measured. The helical cluster had a similarity with a stable helical structure for monomeric Abeta in 2,2,2-trifluoroethanol (TFE)/water determined by an NMR experiment: The positions of helices in the helical cluster were the same as those in the NMR structure, and the residue-residue contact patterns were also similar with those of the NMR structure. The cluster-cluster separation in the conformational space indicates that free-energy barriers separate the clusters at 300 degrees K. The two beta-structural clusters were characterized by different strand-strand hydrogen-bond (H-bond) patterns, suggesting that the free-energy barrier between the two clusters is due to the H-bond rearrangements.