Effective virtual screening protocol for CYP2C9 ligands using a screening site constructed from flurbiprofen and S-warfarin pockets

An effective virtual screening protocol was developed against an extended active site of CYP2C9, which was derived from X-ray structures complexed with flubiprofen and S-warfarin. Virtual screening has been effectively supported by our structure-based pharmacophore model. Importance of hot residues identified by mutation data and structural analysis was first estimated in an enrichment study. Key role of Arg108 and Phe114 in ligand binding was also underlined. Our screening protocol successfully identified 76% of known CYP2C9 ligands in the top 1% of the ranked database resulting 76-fold enrichment relative to random situation. Relevance of the protocol was further confirmed in selectivity studies, when 89% of CYP2C9 ligands were retrieved from a mixture of CYP2C9 and CYP2C8 ligands, while only 22% of CYP2C8 ligands were found applying the structure-based pharmacophore constraints. Moderate discrimination of CYP2C9 ligands from CYP2C18 and CYP2C19 ligands could also be achieved extending the application domain of our virtual screening protocol for the entire CYP2C family. Our findings further demonstrate the existence of an active site comprising of at least two binding pockets and strengthens the need of involvement of protein flexibility in virtual screening.     

C1 and C2-symmetric carbohydrate phosphorus ligands in asymmetric catalysis

Carbohydrates are increasingly used as starting materials for the synthesis of enantiopure ligands. They contain a considerable number of stereocenters, and compounds with all possible configurational combinations are readily available. This tutorial review focuses on ligands obtained by the introduction of phosphorus functionalities (mainly phosphinite, phosphite or phosphine) into a carbohydrate framework. They are classified according to their structural features. In this review, ligands are organised as C1 ligands with a pyranoside or furanoside structure, and C2 ligands. Particular attention is paid to water soluble ligands prepared from carbohydrates. General methods for the preparation of the ligands are presented in order to show how the backbones can be obtained from simple carbohydrates. The catalytic results obtained in commonly studied processes are presented in tables in order to facilitate the comparison between the ligands. The advantages and limitations of the use of ligands based on carbohydrates are discussed.     

Metallatriangles and metallasquares: the diversity behind structurally characterized examples and the crucial role of ligand symmetry

Reports on spontaneous self-assembly processes between metal fragments and organic ligands frequently tend to ignore the fact that the product isolated and structurally characterized in most cases is only one out of a more or less large series of feasible ones. This is true even for rings containing as few as three or four metal ions. Here we shall review metallatriangles and metallasquares containing predominantly cis-square-planar metal entities and a range of bidentate bridging ligands. The most significant features contributing to the number of possible stereoisomers appear to be ligand symmetry and flexibility, viz. rotation of two halves of a ligand about a single bond, or rotation of the whole ligand about the metal-donor atom bonds. With low-symmetry bidentate ligands the number of isomers increases dramatically with ring size as a consequence of an increase in possible connectivity patterns, hence linkage isomers, and an increase in possible rotamer states of the bridging ligands. In this tutorial review it is demonstrated how complexity increases as the symmetry of the bridging ligands is lowered from D(∞h) and D(2h) to C(∞v), C(2v), C(2h) and C(s). Special attention will be paid to cyclic tri- and tetranuclear complexes of substituted pyrimidine ligands (C(2v) and C(s) symmetries) as well as the flexible 2,2'-bipyrazine, which can adopt states of either C(2v) or C(2h) symmetry. Uses of these complexes and ways to reduce the number of isomers will be pointed out.     

Probing polyvalency in artificial systems exhibiting molecular recognition

An approach to the study of polyvalency-the interaction of polyvalent receptors with polyvalent ligands-in unnatural systems is outlined. In this study, the complexation of dibenzylammonium cations by dibenzo[24]crown-8 or benzometaphenylene[25]crown-8 is utilized as the component receptor-ligand interaction. Two analogous multivalent receptors-each containing either seven dibenzo[24]crown-8 (DB24C8 CLUSTER) or seven benzometaphenylene[25]crown-8 (BMP25C8 CLUSTER) moieties appended to a modified beta-cyclodextrin core-were prepared in moderate yields. For each of these multivalent receptors, complementary mono- and divalent ligands containing one or two dialkylammonium centers, respectively, were prepared in good yields. These ligands contained fluorine atom substituents to allow their interactions with crown ether compounds to be probed by (19)F NMR spectroscopy. The complexation of these monovalent ligands with the DB24C8 CLUSTER and the BMP25C8 CLUSTER was studied by determining the average binding constant (K(AVE)) between the receptors and ligands. The abilities of the crown ether clusters to complex with these monovalent ligands was compared with those of the monovalent crown ethers dibenzo[24]crown-8 and benzometaphenylene[25]crown-8. In both instances, it was found that clustering seven crown ethers together into one molecule is detrimental to the abilities of the crown ether moieties to complex with monovalent dialkylammonium ligands. The complexation of the divalent ligands by the DB24C8 CLUSTER and the BMP25C8 CLUSTER was then studied-again by determining K(AVE)-and their abilities to complex with these ligands was compared with those of their respective component interactions. By determining K(AVE) for the polyvalent interaction, it was possible to calculate an association constant, K(POLY), for the binding of the divalent ligands by the DB24C8 CLUSTER and the BMP25C8 CLUSTER compounds. In both instances K(POLY) for the polyvalent interaction was found to be approximately 2 orders of magnitude higher than the association constants, K(A), for the component interaction.     

Catalytic Behavior of Mono-N-Protected Amino-Acid Ligands in Ligand-Accelerated C−H Activation by Palladium(II)

Mono-N-protected amino acids (MPAAs) are increasingly common ligands in Pd-catalyzed C−H functionalization reactions. Previous studies have shown how these ligands accelerate catalytic turnover by facilitating the C−H activation step. Here, it is shown that MPAA ligands exhibit a second property commonly associated with ligand-accelerated catalysis: the ability to support catalytic turnover at substoichiometric ligand-to-metal ratios. This catalytic role of the MPAA ligand is characterized in stoichiometric C−H activation and catalytic C−H functionalization reactions. Palladacycle formation with substrates bearing carboxylate and pyridine directing groups exhibit a 50–100-fold increase in rate when only 0.05 equivalents of MPAA are present relative to Pd^II. These and other mechanistic data indicate that facile exchange between MPAAs and anionic ligands coordinated to Pd^II enables a single MPAA to support C−H activation at multiple Pd^II centers.     

Rationally designed ligands that inhibit the aggregation of large gold nanoparticles in solution

Hexadecanethiol (n-C16), 2,2-dimethylhexadecane-1-thiol (DMC16), and the multidentate thiol-based ligands 2-tetradecylpropane-1,3-dithiol (C16C2), 2-methyl-2-tetradecylpropane-1,3-dithiol (C16C3), and 1,1,1-tris(mercaptomethyl)pentadecane (t-C16) were evaluated for their ability to stabilize large gold nanoparticles (>15 nm) in organic solution. Citrate-stabilized gold nanoparticles (20-50 nm) treated with the ligands were extracted from aqueous solution and dispersed into toluene. The degree of aggregation of the gold nanoparticles was monitored visually and further confirmed by UV-vis spectroscopy and dynamic light scattering (DLS). The bidentate ligands (C16C2 and C16C3) and particularly the tridentate ligand (t-C16) showed enhanced abilities to inhibit the aggregation of large gold nanoparticles in organic solution. For gold nanoparticles modified with these multidentate ligands, bound thiolate (S2p3/2 binding energy of 162 eV) was the predominant sulfur species (>85%) as evaluated by X-ray photoelectron spectroscopy (XPS). Although an entropy-based resistance to ordering of the loosely packed surfactant layers was initially considered to be a plausible mechanism for the enhanced stabilization afforded by the multidentate ligands, when taken as a whole, the data presented here support a model in which the enhanced stabilization arises largely (if not solely) from the multidentate chelate effect.     

General Enantioselective C−H Activation with Efficiently Tunable Cyclopentadienyl Ligands

Cyclopentadienyl (Cp) ligands enable efficient steering of various transition‐metal‐catalyzed transformations, in particular enantioselective C−H activation. Currently only few chiral Cp ligands are available. Therefore, a conceptually general approach to chiral Cp ligand discovery would be invaluable as it would enable the discovery of applicable Cp ligands and to efficiently and rapidly vary and tune their structures. Herein, we describe the three‐step gram‐scale synthesis of a structurally diverse and widely applicable chiral Cp ligand collection (JasCp ligands) with highly variable and adjustable structures. Their modular nature and their amenability to rapid structure variation enabled the efficient discovery of ligands for three enantioselective Rh^III‐catalyzed C−H activation reactions, including one unprecedented transformation. This novel approach should enable the discovery of efficient chiral Cp ligands for various further enantioselective transformations.     

Characterization of C18-bonded liquid chromatographic stationary phases by Raman spectroscopy: the effect of temperature

This study represents the first time that both the mobile phase composition and the temperature are simultaneously controlled to examine silica-bonded octadecylsilyl (C18) ligands spectroscopically at typical liquid chromatographic (LC) mobile phase flow-rates and back-pressures. Raman spectroscopy is used to characterize the behavior of the C18 bonded ligands equilibrated at temperatures from 45 to 2 degrees C in neat, single-component, mobile phase solvents including: water, acetonitrile, methanol, and chloroform. In addition, the effect of stationary phase ligand bonding density is examined by using two different monomeric reversed-phase liquid chromatographic (RPLC) stationary phases, a 2.34 and a 3.52 micromol m(-2) Microporasil C18 stationary phase, under identical conditions. The direct, on-column, spectroscopic analysis used in this study allows direct evaluation of the temperature-dependent behavior of the bonded C18 ligands. The temperature-dependent ordering of the stationary phase ligands is examined to determine if the ligands undergo a phase transition from a less-ordered "liquid-like" state at higher temperatures to a more-ordered "solid-like" state at lower temperatures. A discrete phase transition was not observed, but rather a continual ordering as temperature was lowered.     

Catalytic Behavior of Mono‐N‐Protected Amino‐Acid Ligands in Ligand‐Accelerated C−H Activation by Palladium(II)

Mono‐N‐protected amino acids (MPAAs) are increasingly common ligands in Pd‐catalyzed C?H functionalization reactions. Previous studies have shown how these ligands accelerate catalytic turnover by facilitating the C?H activation step. Here, it is shown that MPAA ligands exhibit a second property commonly associated with ligand‐accelerated catalysis: the ability to support catalytic turnover at substoichiometric ligand‐to‐metal ratios. This catalytic role of the MPAA ligand is characterized in stoichiometric C?H activation and catalytic C?H functionalization reactions. Palladacycle formation with substrates bearing carboxylate and pyridine directing groups exhibit a 50–100‐fold increase in rate when only 0.05 equivalents of MPAA are present relative to Pd^II. These and other mechanistic data indicate that facile exchange between MPAAs and anionic ligands coordinated to Pd^II enables a single MPAA to support C?H activation at multiple Pd^II centers.     

Chiral Proline‐Based P,O and P,N Ligands for Iridium‐Catalyzed Asymmetric Hydrogenation

Two new classes of proline‐based P,O and P,N ligands were prepared and applied in the iridium‐catalyzed asymmetric hydrogenation of alkenes. Both types of ligands induced high enantioselectivities in the hydrogenation of trisubstituted C?C bonds. Iridium complexes derived from P,O ligands bearing sterically demanding amide or urea groups at the pyrrolidine N‐atom proved to be especially efficient catalysts for the conjugate reduction of α,β‐unsaturated esters and ketones, whereas analogous P,N ligands led to better results with dialkyl‐phenyl‐substituted alkenes and an allylic alcohol as substrates.     

Chiral phosphine-phosphoramidite ligands in asymmetric catalysis

Chiral phosphine-phosphoramidite ligands, featuring ready availability, easy modification, and stability towards air and moisture, have recently emerged as a new kind of robust ligands for asymmetric catalysis. They have been found to display wide utilities in various catalytic asymmetric reactions, giving excellent enantioselectivities in the Rh-, Ru-, and Ir-catalyzed asymmetric hydrogenation of C?C, C?O, and C?N double bonds; Rh-catalyzed asymmetric hydroformylation; Pd-catalyzed asymmetric hydrophosphorylation; Pd-catalyzed asymmetric allylic alkylation; Ag-catalyzed asymmetric [3 + 2] cycloaddition; and Cu-catalyzed conjugate addition and reduction. In this review, the progress on the development of chiral phosphine-phosphoramidite ligands in asymmetric catalysis has been summarized.     

Synthesis and coordination chemistry of macrocyclic ligands featuring NHC donor groups

Poly-NHC (NHC = N-heterocyclic carbene) ligands emerged almost immediately after the first stable NHCs had been described. Macrocyclic ligands, featuring NHC donor groups and their metal complexes, however, remained rare until recently. This perspective highlights modern developments in the fields of synthesis and coordination chemistry of macrocyclic poly-NHC ligands. These include the synthesis of tetracarbene ligands which were obtained from complexes of β-functionalized isocyanides followed by cyclization of the coordinated iscocyanide ligands to NH,NH-functionalized NHCs and the subsequent metal template controlled bridging alkylation of the NH,NH-NHCs to yield the macrocycle. The template synthesis of ligands featuring a mixed NHC/phosphine donor set like [11]ane-P(2)C(NHC) and [16]ane-P(2)C(NHC)(2) by linkage of NH,NH-NHCs to different phosphines is also presented. Finally, methods for the preparation of cyclic polyazolium salts, their deprotonation and metalation and the different modes of coordination of such macrocyclic poly-NHC ligands are discussed.     

Synthesis of a new class of chiral 1,5-diphosphanylferrocene ligands and their use in enantioselective hydrogenation

A new family of ferrocenylphosphane ligands has been prepared. Their flexible synthesis allows many structural modifications. The asymmetric induction of these ligands was examined in the hydrogenation of functionalized C=C, C=O, and C=N bonds. The enantioselectivity of the reaction was strongly dependent on the substituent R at the position alpha to the ferrocene moiety. In many cases, both enantiomeric beta-hydroxyesters of the reduction product can be obtained by simply replacing a dimethylamino group in the ligand with a methyl group.     

Dumbbell-Shaped 2,2’-Bipyridines: Controlled Metal Monochelation and Application to Ni-Catalyzed Cross-Couplings

2,2’-Bipyridine ligands (dsbpys) with dumbbell-like shapes and differently substituted triarylmethyl groups at the C5 and C5’ positions showed high ligand performance in the Ni-catalyzed cross-electrophile coupling and the Ni/photoredox-synergistically catalyzed decarboxylative coupling reactions. The superior ligand effects of dsbpys compared to the conventional bpy ligands were attributed to the monochelating nature of dsbpys.     

Asymmetric Pd(II)-Catalyzed C−O,C−N,C−C Bond Formation Using Alkenes as Substrates: Insight into Recent Enantioselective Developments

This Review summarizes the advances in the catalytic enantioselective mono- and difunctionalization of alkenes, highlighting the fundamental role of ligands. Several types of asymmetric reactions have been developed involving different bonds formation, C−O, C−N and C−C, highlighting the urgency to go ahead in the search for new ligands and synthetic methodologies in order to improve the control over the reaction selectivity and activity and thus, to increase the applications in the synthesis of heterocyclic scaffolds and biologically active compounds. The Review is organized into paragraphs, which discuss the type of bond formed during the nucleopalladation, C−O, C−N, C−C bonds, and the type of reaction involved.     

Selective G-quadruplex DNA stabilizing agents based on bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine

Various biologically relevant G-quadruplex DNA structures offer a platform for therapeutic intervention for altering the gene expression or by halting the function of proteins associated with telomeres. One of the prominent strategies to explore the therapeutic potential of quadruplex DNA structures is by stabilizing them with small molecule ligands. Here we report the synthesis of bisquinolinium and bispyridinium derivatives of 1,8-naphthyridine and their interaction with human telomeric DNA and promoter G-quadruplex forming DNAs. The interactions of ligands with quadruplex forming DNAs were studied by various biophysical, biochemical, and computational methods. Results indicated that bisquinolinium ligands bind tightly and selectively to quadruplex DNAs at low ligand concentration (～0.2-0.4 μM). Furthermore, thermal melting studies revealed that ligands imparted higher stabilization for quadruplex DNA (an increase in the T(m) of up to 21 °C for human telomeric G-quadruplex DNA and >25 °C for promoter G-quadruplex DNAs) than duplex DNA (ΔT(m) ≤ 1.6 °C). Molecular dynamics simulations revealed that the end-stacking binding mode was favored for ligands with low binding free energy. Taken together, the results indicate that the naphthyridine-based ligands with quinolinium and pyridinium side chains form a promising class of quadruplex DNA stabilizing agents having high selectivity for quadruplex DNA structures over duplex DNA structures.     

Synthesis of New Chiral Phosphine Ligands and Their Application in Asymmetric Hydrogenation of Ketones

The design of new chiral ligands is the key in the development of transition metal catalyzed asymmetric synthesis. Many chiral diphosphine ligands have been prepared and applied in asymmetric catalytic reactions with excellent enantioselectivities. Among the chiral diphosphine ligands that have been reported, the atropisomeric C2-symmetric phosphines with a biaryl scaffold initiated by Noyori and co-workers with BINAP were found to have the widest application in the transition metal catalyze…     

手性配体在钯催化不对称碳氢键活化反应中的应用

目前,手性配体辅助钯催化的区域和对映选择性碳氢键活化是过渡金属催化的前沿领域.在过去的十年中,它作为一种越来越重要的合成工具,用于合成含有各种不对称元素(中心手性、轴手性和平面手性)的手性分子,也是快速构建各种碳碳键和碳杂原子键的最有效方法之一.本文介绍了一些典型手性配体在钯催化不对称sp2和sp3碳氢键活化/官能团化...     

Recent Advances in the Schiff Bases and N‐Heterocyclic Carbenes as Ligands in the Cross‐Coupling Reactions: A Comprehensive Review

Cross‐coupling reactions, namely, the Suzuki–Miyaura, Heck, Sonogashira, Hiyama, Negishi, Kumada, and Hartwig–Buchwald, are the most powerful approaches in the formation of C–C, C–N, C–O, and C–S bonds for the complex organic scaffolds in drugs, natural products, organic materials, and fine chemicals. The nitrogen‐based ligands have upper hands in these reactions because they are air stable, inexpensive, and easier to handle than the phosphorous counterparts. In this perspective, Schiff bases and N‐heterocyclic carbenes have been explored extensively in terms of novel design and preparation as ligands in the coupling reactions. Facile recovery and reusability of these ligands make them eco‐friendly and economical. A comprehensive outline on the progress in Schiff bases–metal complexes and NHC–metal complexes that mediated cross‐coupling reactions with recent examples highlighted is reported (160 references).     

Chiral induction in self-assembled helicates: CHIRAGEN type ligands with ferrocene bridging units

The aim of this work was the preparation of enantiomerically pure bis(pinene-bipyridine) ligands containing the ferrocenyl moiety. Several such ligands (1-3) were synthesized and completely characterized. These molecules can be diastereoselectively deprotonated at the acidic methylene group of the pinene moiety using a strong and sterically hindered base such as LDA. Subsequent reaction of the formed anion with alkyl halides yield the family of C(2)-symmetric enantiopure compounds (1a-c). Copper(I), silver(I), or zinc(II) complexes with several ligands (C1-C8) were prepared and structurally characterized in the solid state and in solution. Self-assembled helical species are formed in several cases. It became evident that the chiral groups present in the ligand do not completely determined the helical configuration of the assemblages. Diastereoselectivity is thus not complete with this type of ligands, contrary to other, similar ligands studied before.