BippyPhos: A Highly Versatile Ligand for Pd-Catalyzed C−N,C−O and C−C Couplings

Numerous ligands have been designed for the Buchwald-Hartwig Amination (BHA). Among the ligands developed is BippyPhos. This ligand was originally designed to enable a coupling of primary amines with aryl halides. Further studies showed that the ligand has fairly broad utility for Pd-catalyzed C−N, C−O and C−C couplings. This review describes the various Pd-catalyzed applications involving BippyPhos as a supporting ligand. While BippyPhos may not often be the most optimal ligand for various Pd-catalyzed couplings, it typically will provide adequate results as a starting point prior to screening for optimization.     

Evaluation of solvent accessibility epitopes for different dehydrogenase inhibitors

Knowledge about the orientation of ligands or inhibitors bound to a protein is vital for the development of new drugs. It was recently shown that solvent accessibility epitopes for protein ligands can be mapped by transferring magnetization from water molecules to the ligand to derive the ligand orientation. This is based on the fact that NMR signals of ligands arising from magnetization transferred from solvent molecules via the protein have a different sign from those arising from direct magnetization transfer from bulk water. Herein we critically evaluate the applicability of solvent accessibility mapping to derive binding orientations for ligands of two dehydrogenases (AKR1C3 and HSD17beta1) with very different binding pockets, including complexes in which the ligand is buried more deeply inside the protein. We also evaluate the possibility of using co-solvents, such as DMSO, for magnetization transfer.     

Control of STING Agonistic/Antagonistic Activity Using Amine-Skeleton-Based c-di-GMP Analogues

Stimulator of Interferon Genes (STING) is a type of endoplasmic reticulum (ER)-membrane receptor. STING is activated by a ligand binding, which leads to an enhancement of the immune-system response. Therefore, a STING ligand can be used to regulate the immune system in therapeutic strategies. However, the natural (or native) STING ligand, cyclic-di-nucleotide (CDN), is unsuitable for pharmaceutical use because of its susceptibility to degradation by enzymes and its low cell-membrane permeability. In this study, we designed and synthesized CDN derivatives by replacing the sugar-phosphodiester moiety, which is responsible for various problems of natural CDNs, with an amine skeleton. As a result, we identified novel STING ligands that activate or inhibit STING. The cyclic ligand 7, with a cyclic amine structure containing two guanines, was found to have agonistic activity, whereas the linear ligand 12 showed antagonistic activity. In addition, these synthetic ligands were more chemically stable than the natural ligands.     

亲和仿生层析及在抗体纯化中的应用

亲和仿生层析是一种新型的生物分离技术,可用于生物活性物质分离,尤其在抗体纯化中表现出良好的应用前景,具有价格低廉、结构稳定、特异性较高等优点。亲和仿生层析的核心是具有特定结构的仿生配基,主要包括化学合成配基和短肽配基两种,通常通过合理的手段进行筛选和设计。理性设计是一种行之有效的方法,针对一个特定的目标蛋白,随机地去选择配基是不可能的,必须采用理性设计构建一个合理的配基库,并通过高通量的筛选技术,才能得到合适的仿生配基。本文根据近年来国内外亲和仿生层析的研究进展,着重介绍了亲和仿生配基的筛选和设计以及在抗体纯化中的应用。     

Developing chiral ligands for asymmetric hydrogenation

This Account outlines our efforts in ligand development for asymmetric hydrogenation. The successful development of three classes of ligands is presented, including (1) ligands with phosphocyclic motifs, (2) ligands with atropisomeric backbones, and (3) bisphosphine ligands inspired by the structure of 2,3- O-isopropylidene-2,3-dihydroxyl-1,4-bis(diphenylphosphino)butane (DIOP). With this large ligand toolbox, we have prepared many pharmaceutically valuable chiral products efficiently.     

Dissimilar Ligands Bind in a Similar Fashion: A Guide to Ligand Binding-Mode Prediction with Application to CELPP Studies

The molecular similarity principle has achieved great successes in the field of drug design/discovery. Existing studies have focused on similar ligands, while the behaviors of dissimilar ligands remain unknown. In this study, we developed an intercomparison strategy in order to compare the binding modes of ligands with different molecular structures. A systematic analysis of a newly constructed protein–ligand complex structure dataset showed that ligands with similar structures tended to share a similar binding mode, which is consistent with the Molecular Similarity Principle. More importantly, the results revealed that dissimilar ligands can also bind in a similar fashion. This finding may open another avenue for drug discovery. Furthermore, a template-guiding method was introduced for predicting protein–ligand complex structures. With the use of dissimilar ligands as templates, our method significantly outperformed the traditional molecular docking methods. The newly developed template-guiding method was further applied to recent CELPP studies.     

Asymmetric hydrogenation using monodentate phosphoramidite ligands

Monodentate phosphoramidites are excellent ligands for Rh-catalyzed asymmetric hydrogenations of substituted olefins. Enantioselectivities between 95 and 99% were obtained in the asymmetric hydrogenation of protected alpha- and beta-dehydroamino acids and esters, itaconic acid and esters, aromatic enamides, aromatic enol esters, aromatic and aliphatic enol carbamates, and alpha-substituted cinnamic acids. An iridium catalyst Ir(L*)(COD)Cl was developed that contains only a single bulky phosphoramidite based on 3,3'-disubstituted BINOL or bisphenol as a chiral ligand. With this catalyst, acetylated dehydroamino acid esters could be hydrogenated with very good enantioselectivity. Most reactions have turnover frequencies of 250-1600 h (-1), depending upon the hydrogen pressure. The enantioselectivity is unaffected by the pressure over a wide range. Because of their modularity and easy synthesis, parallel ligand synthesis is possible. Results obtained with these library ligands deviate only slightly from those obtained with purified ligands. Using this instant ligand library protocol, DSM has developed catalysts for industrial processes. These MonoPhos ligands are currently used in production for pharmaceutical intermediates by DSM. It is possible to use catalysts based on a mixture of two different monodentate ligands, such as two different monodentate phosphoramidites or one phosphoramidite and one achiral phosphine ligand. Dependent upon the substrate, the "mixed" catalyst may lead to higher enantioselectivity and rate than the "homocatalysts".     

In situ electrochemical impedance spectroscopy/synchrotron radiation grazing incidence X-ray diffraction—A powerful new technique for the characterization of electrochemical surfaces and interfaces

A marriage of electrochemical impedance spectroscopy (EIS) and in situ synchrotron radiation grazing incidence X-ray diffraction (SR-GIXRD) has provided a powerful new technique for the elucidation of the mechanistic chemistry of electrochemical systems. In this study, EIS/SR-GIXRD has been used to investigate the influence of metal ion buffer calibration ligands, along with natural organic ligands in seawater, on the behaviour of the iron chalcogenide glass ion-selective electrode (ISE). The SR-GIXRD data demonstrated that citrate - a previously reported poor iron calibration ligand for the analysis of seawater - induced an instantaneous and total dissolution of crystalline GeSe and Sb₂Se₃ in the modified surface layer (MSL) of the ISE, while natural organic ligands in seawater and a mixture of ligands in a mimetic seawater ligand system protected the MSL's crystalline inclusions of GeSe and Sb₂Se₃ from oxidative attack. Expectedly, the EIS data showed that citrate induced a loss in the medium frequency time constant for the MSL of the ISE, while seawater's natural organic ligands and the mimetic ligand system preserved the medium frequency EIS response characteristics of the ISE's MSL. The new EIS/SR-GIXRD technique has provided insights into the suitability of iron calibration ligands for the analysis of iron in seawater.     

New carbon- and sulfur-based ligands in catalysis

Homogeneous catalysis is a field of research that has gained central importance in both organic and inorganic chemistry and the use of well-defined ligand systems in the synthesis of transition metal complexes has had an enormous impact on the development of such catalysts. Neutral, two-electron donor ligands based on phosphorous and nitrogen have been tremendously successful as ancillary entities for late-transition metal (LTM) catalysts, whereas ligands based on anionic nitrogen, oxygen and the cyclopentadienyl motif (Cp(-)) have propelled early-transition metal (ETM) catalysis forward. We believe that expanding the ligand families capable of acting as successful entities in metal-mediated reactivity and catalysis is crucial for future discoveries in this field. Research in our group therefore tries to identify new non-chiral and chiral ligands for late-transition metal chemistry that are based on neutral, two-electron carbon and sulfur donor atoms. In particular, we have until now focused on the development of modular, monodentate N-heterocyclic carbene ligands (NHCs) that can serve as a basis for the development of chiral ligand frameworks for the application to asymmetric catalytic transformations. In the second major research project developed over the last six years, we have started an investigation on the use of chelating sulfoxide-based ligands in asymmetric late transition-metal based catalysis.     

Tuning the Peri Effect for Enantioselectivity: Asymmetric Hydrogenation of Unfunctionalized Olefins with the BIPI Ligands

The modular nature of the BIPI ligands allows for systematic optimization of each ligand region. The development of ligands optimized for asymmetric hydrogenation of the challenging unfunctionalized olefin substrate class is described. The naphthyl peri position, C‐8, has been identified as a critical stereocontrol element in the design of these ligands. Highly enantioselective ligands suitable for hydrogenation of tri‐ and tetrasubstituted olefins are detailed.     

Effect of ligand chain length on hydrophobic charge induction chromatography revealed by molecular dynamics simulations

Hydrophobic charge induction chromatography (HCIC) is a mixed-mode chromatography which is advantageous for high adsorption capacity and facile elution. The effect of the ligand chain length on protein behavior in HCIC was studied. A coarse-grain adsorbent pore model established in an earlier work was modified to construct adsorbents with different chain lengths, including one with shorter ligands (CL2) and one with longer ligands (CL4). The adsorption, desorption, and conformational transition of the proteins with CL2 and CL4 were examined using molecular dynamics simulations. The ligand chain length has a significant effect on both the probability and the irreversibility of the adsorption/desorption. Longer ligands reduced the energy barrier of adsorption, leading to stronger and more irreversible adsorption, as well as a little more unfolding of the protein. The simulation results elucidated the effect of the ligand chain length, which is beneficial for the rational design of adsorbents and parameter optimization for high-performance HCIC.     

Hydroformylation Catalysis at Eastman Chemical: Generations of Catalysts

Eastman Chemical has a long term hydroformylation research program that has resulted in several successful low pressure rhodium catalyst technologies. The history of the bidentate ligand, BISBI, and the more recent development of halophosphite ligands will be discussed. The BISBI ligand is well known for high selectivity to the normal isomer and has been widely discussed in the literature. The relatively unknown halophosphite ligands exhibit a unique ability to produce aldehyde products with a variable range of linear to branched ratios by manipulating reaction variables such as reaction temperature, ligand concentration or carbon monoxide partial pressure. The halophosphite catalysts have been found to be resistant to poisoning by traditional hydroformylation poisons such as acetylene.     

Development of Computational Approaches with a Fragment-Based Drug Design Strategy: In Silico Hsp90 Inhibitors Discovery

A semi-exhaustive approach and a heuristic search algorithm use a fragment-based drug design (FBDD) strategy for designing new inhibitors in an in silico process. A deconstruction reconstruction process uses a set of known Hsp90 ligands for generating new ones. The deconstruction process consists of cutting off a known ligand in fragments. The reconstruction process consists of coupling fragments to develop a new set of ligands. For evaluating the approaches, we compare the binding energy of the new ligands with the known ligands.     

Photopharmacology of Ion Channels through the Light of the Computational Microscope

The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.     

亲和膜配基的结构和密度对胆红素吸附的影响

体内存在过量的胆红素会引起神经系统疾病,严重时危及生命,常用循环吸附法去除,但是多数胆红素与白蛋白形成复合物,难于拆分,导致血清胆红素的吸附去除率降低。以醋酸纤维素/聚乙烯基亚胺共混亲和膜(CA/PEI膜)为基质,通过戊二醛活化,引入间隔臂,固载具有一定特异性吸附的5种有机胺和8种氨基酸配基,强化血清胆红素的去除效果。研究结果表明,虽然改性膜的伯胺基含量仅为CA/PEI膜的1/3,但是因间隔臂的引入和配基特异性的增强,4种改性膜的胆红素吸附量提高了100%以上,并且提高了胆红素相对于蛋白的吸附选择性。增加胺基和疏水结构有利于胆红素的吸附;羧基不利于胆红素吸附;胆红素吸附还受到配基密度和空间位阻等诸多因素的影响。苯环等空间位阻较大的配基,不利于实际胆红素的吸附,且无法通过提高配基密度而提高其改性膜的胆红素吸附量,而含直链胺配基的己二胺(3-HMD)改性膜的胆红素吸附量随配基密度的提高而提高。     

Design,Synthesis and X-Ray Structural Studies of Potent HIV-1 Protease Inhibitors Containing C-4 Substituted Tricyclic Hexahydro-Furofuran Derivatives as P2 Ligands

The design, synthesis, X-ray structural, and biological evaluation of a series of highly potent HIV-1 protease inhibitors are reported herein. These inhibitors incorporate novel cyclohexane-fused tricyclic bis-tetrahydrofuran as P2 ligands in combination with a variety of P1 and P2′ ligands. The inhibitor with a difluoromethylphenyl P1 ligand and a cyclopropylaminobenzothiazole P2′ ligand exhibited the most potent antiviral activity. Also, it maintained potent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The corresponding inhibitor with an enantiomeric ligand was significantly less potent in these antiviral assays. The new P2 ligands were synthesized in optically active form using enzymatic desymmetrization of meso-diols as the key step. To obtain molecular insight, two high-resolution X-ray structures of inhibitor-bound HIV-1 protease were determined and structural analyses have been highlighted.     

Drug Screening Boosted by Hyperpolarized Long‐Lived States in NMR

Transverse and longitudinal relaxation times (T_1ρ and T₁) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long‐lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T₁(¹H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D‐DNP). Hyperpolarized weak “spy ligands” can be displaced by high‐affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput.     

2,4-二羟基苯甲醛的选择性烷基化研究进展

2,4-二羟基苯甲醛是合成Salen催化剂的一种重要的配体,而烷基化不仅是改变这种配体的一种重要手段,而且还是将这种配体进行高分子化的重要方法。所以本文综述了2,4-二羟基苯甲醛的选择性烷基化的一些研究新进展,以期为合成新型Salen催化剂配体奠定理论基础。     

Surface-structure-regulated penetration of nanoparticles across a cell membrane

The cell uptake rate of nanoparticles (NPs) coated with mixed hydrophilic/hydrophobic ligands is known to be strongly influenced by the ligand pattern on the nanoparticle surface. To help reveal the physical mechanism behind this intriguing phenomenon, here we perform dissipative particle dynamics simulations to analyze the evolution of free energy as the ligand-coated NPs pierce through a lipid bilayer. Four characteristic ligand patterns are considered: striated NPs with alternating hydrophilic and hydrophobic groups compared to NPs with randomly mixed ligands at the same hydrophilic to hydrophobic ratio, as well as NPs coated with homogeneous hydrophilic or hydrophobic ligands. The free energy analysis indicates that among the four ligand patterns under study, the striated NP encounters the lowest energy barrier during translocation across the membrane. Further analysis reveals that the translocation of the striated NP is facilitated by the constraint of its rotational degree of freedom by the anisotropic ligand pattern, which prevented the free energy of the system from sinking to a deeper valley as the NP passes through the hydrophobic core of the bilayer. Finally, the critical forces required for almost instant penetration of these patterned NPs across the bilayer are calculated and shown to be consistent with the free energy analysis. These findings provide useful guidelines for the molecular design of patterned NPs for controllable cell penetrability.