胰蛋白酶定向固定化亲和配基的理性设计

在胰蛋白酶三维(3D)结构的基础上, 首先利用分子对接从ZINC 数据库中筛选获得了与胰蛋白酶具有较高亲和性的小分子配基2-硝基苯基-β-D-葡糖苷, 并分析了该配基与蛋白质之间的相互作用力主要为范德华和氢键相互作用. 并利用分子动力学模拟进一步验证了2-硝基苯基-β-D-葡糖苷与胰蛋白酶之间具有较强的亲和作用. 分子动力学(MD)模拟结果表明, 配基-目标蛋白质之间形成稳定的复合物且它们之间的距离基本没有变化. 此外, 一个水分子通过氢键在配基和目标蛋白质的结合腔之间架桥. 最后制备了偶联有该配基的亲和载体, 进行了胰蛋白酶的定向固定化, 并考察了该固定化酶的活性. 研究结果表明, 利用修饰2-硝基苯基-β-D-葡糖苷配基的亲和载体固定化胰蛋白酶的酶活达到340.8 U·g^-1, 比活达到300.3 U·mg^-1, 分别是未修饰亲和配基载体的10倍和5倍, 具有明显的优势. 上述结论证明了结合分子对接和分子动力学模拟理性设计定向固定化亲和配基的方法是可行的, 具有一定的理论和实用价值.     

How bulky ligands control the chemoselectivity of Pd-catalyzed N-arylation of ammonia

Steric bulk has been recognized as a central design principle for supporting ligands in the widely utilized Buchwald–Hartwig amination. In a recent example, it was shown that a Pd-catalyst carrying a phosphine ligand can successfully aminate aryl halides using ammonia as the nitrogen source. Interestingly, the chemoselectivity of this reaction was found to depend on the steric demand of the phosphine ligand. Whereas a sterically less demanding phosphine affords diphenylamine as the major product, it was shown that the amination reaction can be stopped after the first amination to give aniline if a sterically more encumbering phosphine ligand is used. Density functional theory calculations were carried out to examine the relationship between the steric demand of the phosphine ligand and the chemoselectivity. It was found that the key feature that leads to the chemoselectivity is the ability of the phosphine ligand to rotate the biaryl moiety of the ligand away from the Pd-center upon amine addition to release some of the steric crowding from the Pd-coordination site.

Steric bulk has been recognized as a central design principle for ligands in the widely utilized Buchwald–Hartwig amination. This mechanistic study reveals how this steric effect manipulates the reaction pathway and determines the chemoselectivity.     

Tetradentate schiff base ligand/MCln initiating systems for the controlled cationic polymerization of isobutyl vinyl ether: Effects of the ligand framework

We investigated the cationic polymerization of vinyl ethers using metal complex catalysts with salen and salphen ligands. Metal complexes were generated in situ from the reaction of a ligand and a metal chloride. The choice of a ligand and a central metal was crucial for tuning the catalyst function such as catalytic activity and controllability of the polymerization. Among metal chlorides employed, ZrCl₄ was the most efficient for controlled polymerization. Cationic polymerization of isobutyl vinyl ether (IBVE) proceeded using the salen and salphen‐type ligand/ZrCl₄ initiating systems, yielding polymers with predetermined molecular weights and narrow molecular weight distributions. Importantly, the structural effects of the complex catalysts were responsible for the polymerization behavior. For example, the polymerization using the salen‐type ligand/ZrCl₄ system was much slower than that using the salphen‐type ligand/ZrCl₄ system. In addition, the polymerization of IBVE using the salen‐type ligand/FeCl₃ system proceeded in a controlled manner, which was in contrast to uncontrolled polymerization using the salphen‐type ligand/FeCl₃ system. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2019 , 57, 989–996     

GalaxyDock3: Protein–ligand docking that considers the full ligand conformational flexibility

Predicting conformational changes of both the protein and the ligand is a major challenge when a protein–ligand complex structure is predicted from the unbound protein and ligand structures. Herein, we introduce a new protein–ligand docking program called GalaxyDock3 that considers the full ligand conformational flexibility by explicitly sampling the ligand ring conformation and allowing the relaxation of the full ligand degrees of freedom, including bond angles and lengths. This method is based on the previous version (GalaxyDock2) which performs the global optimization of a designed score function. Ligand ring conformation is sampled from a ring conformation library constructed from structure databases. The GalaxyDock3 score function was trained with an additional bonded energy term for the ligand on a large set of complex structures. The performance of GalaxyDock3 was improved compared to GalaxyDock2 when predicted ligand conformation was used as the input for docking, especially when the input ligand conformation differs significantly from the crystal conformation. GalaxyDock3 also compared favorably with other available docking programs on two benchmark tests that contained diverse ligand rings. The program is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html . © 2019 Wiley Periodicals, Inc.     

A novel C2-symmetric bisphosphane ligand with a chiral cyclopropane backbone: synthesis and application in the Rh(I)-catalyzed asymmetric 1,4-addition of arylboronic acids

The synthesis of a novel C₂-symmetric bisphosphane ligand was accomplished starting from trans-(2R,3R)-bis(3′,5′-diphenylphenyl)cyclopropane-1,1-dimethanol as a key intermediate. This ligand was tested in the asymmetric rhodium(I)-catalyzed 1,4-addition to cyclic enones. We also compared the new ligand with a similar phosphane ligand with a less bulky cyclopropane backbone. Good yields (up to 99%) and enantioselectivities (up to 89% ee) were observed. We demonstrated that the presence of a more bulky cyclopropane backbone resulted in a less effective ligand.     

The preparation of a stable 2-pyridylboronate and its reactivity in the Suzuki-Miyaura cross-coupling reaction

The preparation and reactivity of a 2-pyridylboronate stabilised by N-phenyldiethanolamine is described. In Suzuki-Miyaura cross-coupling reactions employing this boronate, significant aryl-aryl exchange from the phosphine ligand was observed with some combinations of ligand and substrates. The amount of the exchange by-product can be minimised by appropriate choice of phosphine ligand.     

Regulation of the flexibility of planar chiral [2.2]paracyclophane ligands and its significant impact on enantioselectivity in asymmetric reactions of diethylzinc with carbonyl compounds

A series of planar chiral ligands derived from [2.2]paracyclophane were synthesized and applied as catalysts in enantioselective additions of diethylzinc to aldehydes and α,β-unsaturated ketones. When ligand 10 with a dimethyl hydroxymethyl as the substituent was used, the enantioselectivity of the reaction of diethylzinc with aldehydes was much higher than when using ligand 3c with diphenyl hydroxymethyl as the substituent. The situation was the same with the 1,4-addition of diethylzinc to α,β-unsaturated ketones with 63–83% ee being obtained when the hydroxymethyl substituted ligand 7b was used, while almost no enantioselectivity was afforded if ligand 3c was used. The role of planar chirality is also studied.     

Resolution in Affinity Chromatography the Effect of the Heterogeneity of Immobilized Soybean Trypsin Inhibitor on the Separation of Pancreatic Proteases

By affinity chromatography, trypsins and chymotrypsins from mouse pancreas homogenates have been separated using soybean trypsin inhibitor immobilized on Sepharose. The effects of the functional heterogeneity of the adsorbent have been investigated in terms of the resolution obtained. Heterogeneity has been found to originate from the following sources: heterogeneity of the ligand before immobilization; alteration of the ligand by immobilization; and modification of the ligand after immobilization by molecules to be fractionated. Only when the heterogeneity of the adsorbent was minimized could the resolution of closely related enzyme species be achieved. The elution conditions for different enzymes depended on the amount of enzyme applied, as no complete homogeneity could be obtained. In addition, it was found that the adsorbent was partly degraded by the pancreas extract, reducing its fractionating capacity.     

Vertical distribution and potential sources of strong ligands for copper(II) in the North Pacific

Complexing ability of natural organic ligands in seawater was determined by an approach based on coordination chemistry, i.e., thermodynamic calculations of the conditional stability constants of remarkably stable copper(II) complexes of natural ligands, which were maintained against the ligand-exchange reaction with a large excess of ethylenediaminetetraacetic acid. There exist strong ligands with the conditional stability constant of log K’_CuL > 14 at pH 5.71 and 4°?C ubiquitously in non-living dissolved organic matter, concentrated from both coastal and oceanic regimes. This type of ligand was detected at most depths from surface to 1,000 m in the oceanic regimes. The same appraoch was applied to a sample of marine organism (phytoplankton) and the strong ligand class was found out in phytoplankton. It is suggested that phytoplankton may be one of potential sources for the strong ligand.     

Interpretation of the parameters of the EPR spectra of complexes containing ns 1 ions

The parameters of the EPR spectra of complexes containing paramagnetic ions with an unpaired ns electron (ns ¹ ions) were interpreted. The effect of the ligand spin-orbital coupling on the parameter of the Zeeman splitting was discussed. The effect of spin polarization on the parameters of hyperfine and ligand hyperfine couplings was considered. The reasons for the anomalous behavior of the EPR parameters were noted. The character of the covalent bonding was analyzed from the EPR spectra. The anomalous behavior of the parameters of ligand hyperfine couplings in tetragonal complexes with ns ¹ ions was discussed.     

Ligand coordinate analysis of SC-558 from the active site to the surface of COX-2: a molecular dynamics study

We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published crystal structure of COX-2 with SC-558 in the active site (1cx2) was taken, and the ligand was moved incrementally in 13 steps. At each of these points on the path, exhaustive minimization and dynamics calculations were performed. The role of water was found to be important in these computations. An average structure was obtained from 250 conformations at each point and minimized. At each point on the path, the 10 lowest-energy conformations were also selected; a consideration of the average and lowest conformations provides fine details on the consistency of specific and strong interactions, and also on the geometry of the ligand. The movement of the ligand through the protein may be divided into three stages that are distinguished from each other because of energy and geometry discontinuities in both the ligand and the protein. The first of these covers the region between the active site and the point at 5.8 A from it. The second, which covers the distance between 8.2 and 10.0 A and is associated with maximum energetic and structural instability, is of critical importance. The third stage covers the distance between 10.5 A and the exterior and represents a stage of increasing hydration and expulsion of the ligand from the protein. Our results provide a confirmation for the existence of a shallow cavity near the protein surface in which the ligand is bound reversibly. By examining the residues that show maximum mobility, one obtains an idea of the gating mechanism that governs the entry and exit of the protein into or from the deep pocket that contains the active site. We note, however, that the variation of the root-mean-square deviation of all residues begins to increase almost as soon as the ligand leaves the active site, and even before there are any changes in the gate inter-residue distances. This loosening of the protein even before the gate opens might be a part of the enthalpy-entropy balance that accompanies the ligand's passage through the protein. Our results provide an energy profile of the ligand during its entry/exit into/from the protein and can, in principle, enable one to assess the residence time, which in turn may be associated or indirectly correlated with adverse cardiovascular side effects of nonsteroidal anti-inflammatory drugs. We believe that similar analyses for other selected COX-2-specific inhibitors will provide a measure (or prediction) of possible toxicity effects.     

Application of the FCP-activation procedure to the synthesis of a biospecific adsorbent for trypsin

The synthesis of a biospecific adsorbent for trypsin was chosen as a model to investigate the applicability of FCP activation in affinity chromatography.p-Aminobenzamidine was chosen as a ligand, directly suitable for immobilization. The nonspecific binding properties of the first series of synthesized agarose derivatives were obviated either by FCP activation of the ligand instead of the matrix, or by modifying the initial FCP-activation procedure. The adsorbents prepared in this way, however, demonstrated no selectivity between trypsin and chymotrypsin. The introduction ofe-aminocaproic acid as a spacer was ineffectual. These problems were solved by the application of glycylglycine as a spacer. The final affinity matrices had a degree of substitution of approximately 4 μ.mol of ligand per gram gel (100 μmol ligand per gram dry adsorbent). The specific activity of a current trypsin preparation was increased by 58% in a single cycle. The biospecificity of these adsorbents was demonstrated.     

Spectrophotometric determination of the formation constants of some transition metal cations with a new synthetic Schiff base in dichloromethane and chloroform using rank annihilation factor analysis

The complex formation between a new synthesized Schiff base and the cations Ni²⁺, Co²⁺, Cu²⁺, Zn²⁺ in dichloromethane (DCM) and chloroform solutions was investigated spectrophotometrically using rank annihilation factor analysis (RAFA). The results of mole ratio plots and continuous variation data show the stoichiometry of complexation were found to be 1:1, and 2:1 metal ion to ligand. The stoichiometry was obtained as 1:1 metal ion to ligand ratio for Co²⁺, Ni²⁺ and Zn²⁺ in chloroform and 2:1 for Cu²⁺. In DCM the stoichiometry was obtained as 1:1 for Co²⁺ and 2:1 for Ni²⁺ and Zn²⁺ and a consecutive 2:1 metal ion to ligand ratio was obtained for Cu²⁺. Formation constants of these complexes were estimated by application of RAFA on spectrophotometric data. In this process the contribution of ligand was removed from the absorbance data matrix when the complex stability constant acts as an optimizing object and simply combined with the pure spectrum of the ligand, the rank of the original data matrix can be reduced by one by annihilating the information of the ligand from the original data matrix.     

Computational study of the cyclopalladation mechanism of azobenzene with PdCl2 in N,N-dimethylformamide

The mechanism of cyclopalladation of azobenzene (L) with PdCl₂ in N,N-dimethylformamide (dmf) was studied computationally, using DFT (B3LYP) methods supplemented with a continuum solvation model. Since the exact nature of the reacting complex is unknown, several candidates were considered. These were: (1) a mononuclear adduct with two ligand molecules, L-PdCl₂-L, (2) a mononuclear adduct with one ligand and one solvent molecule, L-PdCl₂-dmf, (3) a dinuclear adduct with a double chloride bridge, [L-PdCl-(μ-Cl)]₂, and (4) a coordinatively unsaturated complex with an agostic interaction, L-PdCl₂. The reaction profile initiating from L-PdCl₂-dmf, which displays an agostic intermediate produced after displacement of the dmf molecule by the activating C-H bond, has the lowest barrier (20.4 kcal/mol in the step with the proton transfer to the O(dmf) atom). In all other reaction pathways, the proton migration is to a chlorine atom and is associated with remarkably high barriers. The results are related to previous experimental and other computational findings. While none of the reaction profiles includes explicit dissociation of the ligand, the proton transfer was found to occur only after the ligand is almost completely displaced from the coordinating shell. It was concluded that the transition state corresponds to 14-electron coordination of Pd and that ease of a ligand dissociation is an important, but not necessarily decisive, factor for cyclopalladation.     

Fast NMR‐Based Determination of the 3D Structure of the Binding Site of Protein–Ligand Complexes with Weak Affinity Binders

In early drug discovery approaches, screening hits are often weak affinity binders that are difficult to characterize in structural detail, particularly towards obtaining the 3D structure of protein–ligand complexes at atomic resolution. NMR is the outstanding technique to tackle such problems, yet suffers from a tedious structure calculation process. N MR² was recently developed to alleviate the laborious element of routine NMR structure calculation procedures and provides the structural information at protein–ligand interaction sites orders of magnitude faster than standard procedures. The N MR² method was extended to weak binders and applied to the oncoproteins HDM2 and MDMX. The structure of the MDMX‐SJ212 complex is reported with a K _d of approximately 0.7 μm ; the complex structure of HDM2 with the mm affinity ligand #845 exhibits a new scaffold.     

Temperature‐responsive Catalyst for the Coupling Reaction of Carbon Dioxide and Propylene Oxide

The selective synthesis of polypropylene carbonate (PPC) and cyclic propylene carbonate (CPC) from coupling reaction of CO₂ and propylene oxide (PO) is a long term pursuing target. Here we report that a temperature controllable porphyrin aluminum catalyst using 5,10,15,20‐tetra(1,2,3,4,5,6, 7,8‐octahydro‐1,4:5,8‐dimethanoanthracen‐9‐yl)porphyrin as ligand, once in conjunction with suitable onium salt, achieved single cycloaddition or copolymerization reaction. Only cycloaddition reaction happened at temperature above 75 °C to produce 100% CPC, whereas copolymerization became dominant to afford PPC with selectivity over 99% at 25 °C, and the obtained PPC showed over 99% carbonate linkage and 92% head‐to‐tail structure. Based on systematic analysis of the electronic and steric feature in the porphyrin ligand, it was found that the electronic feature of the substituent in porphyrin ligand was decisive for PPC selectivity, porphyrin ligand bearing strong electron‐donating substituents displayed a significantly reduced tolerance towards increased temperature with respect to PPC formation. Therefore, temperature‐responsive catalyst could be designed by suitable modification in porphyrin ligand, and such accurate synthesis of target product by one catalyst may create a useful and facile platform for selective PPC or CPC production.     

Study of the spectroscopic characteristics of methyl (ligand) cobaloximes and their antibacterial activity

Spectroscopic characterization (IR, NMR and electronic spectra) of methyl (ligand) cobaloxime was done, where ligand = pyrazole, dimethyl pyrazole, alanine and alanine methyl ester. The frequency changes in the IR spectra and shifts in the NMR were explained on the basis of basicity of the ligand, steric hindrance, HSAB principle and dπ-pπ back-bonding from metal to ligand. Alanine and alanine methyl ester form more stable complexes than pyrazole and dimethyl pyrazole. Based on their IR and ¹H NMR spectra it is inferred that pyrazole and dimethylpyrazole bind to Co (III) via N-2 ring nitrogen, i.e. monodentate coordination.     

Pd(II)-catalyzed and diethylzinc-mediated asymmetric umpolung allylation of aldehydes in the presence of chiral phosphine-Schiff base type ligands

Chiral phosphine-Schiff base type ligand L3 prepared from (R)-(?)-2-(diphenylphosphino)-1,1′-binaphthyl-2′-amine was found to be a fairly effective chiral ligand for the Pd(II)-catalyzed and diethylzinc-mediated enantioselective umpolung allylation of aldehydes to give homoallylic alcohols in good yields, moderate enantioselectivities and high syn diastereoselectivities.     

On the interaction of two different types of ligands binding to the same molecule part I: basics and the transfer of the decoupled sites representation to systems with n and one binding sites

The decoupled sites representation (DSR) for one type of ligand allows to regard complex overall titration curves as sum of classical Henderson-Hasselbalch (HH) titration curves. In this work we transfer this theoretical approach to molecules with different types of interacting ligands (e.g. protons and electrons), prove the existence of decoupled systems for n ₁ and one binding sites for two different ligands, and point out some difficulties and limits of this transfer. A major difference to the DSR for one type of ligand is the loss of uniqueness of the decoupled system. However, all decoupled systems share a unique set of microstate probabilities and each decoupled system corresponds to a certain permutation of these microstate probabilities. Moreover, we show that the titration curve of a certain binding site in the original system can be regarded as linear combination of the titration curves of the individual sites of the decoupled system if the weights of the linear combination are substituted by functions in the activity of the second ligand. In the underlying model with only pairwise interaction, an important observation of our theoretical investigation is the following: Even though the binding sites of ligand L ₁ may not interact directly, they can show secondary interaction due to the interaction with the second type of ligand. This means, if the activity of the second ligand is fixed and we regard the 1-dimensional titration curve of an individual binding site for ligand L ₁ depending on its activity, we may observe a strong deviation from the classical HH shape in spite of non-interacting sites for ligand L ₁.     

二氧化硅固载Ru基催化剂上二氧化碳加氢合成甲酸的研究(III): 配体对催化剂反应性能的影响

考察了不同配体对原位合成的固载Ru基催化剂上CO₂加氢合成HCOOH反应活性的影响, 对于以单齿三苯基类ZPh₃分子为配体的催化剂, 活性大小顺序为: PPh₃＞AsPh₃＞NPh₃. 以PPh₃为配体时, 其相应的原位合成催化剂上HCOOH的TOF值为656 h^－1. 其次, 双齿膦配体的使用能带来比单齿膦配体更高的活性. 以dppe [1,2-双(二苯基膦基)乙烷]为配体时, 其相应的原位合成催化剂上HCOOH的TOF值为1190 h^－1. 量子化学的理论计算结果表明, 具有适中的σ给予性和π接受性, 较小的空间位阻, 较好的电子离域作用的PPh₃配体性能优于其它单齿三苯基类配体. 而具有较好的电子离域作用, 并且有螯合作用的双齿膦配体性能优于单齿膦配体.