Structural and Dynamic Basis of Human Cytochrome P450 7B1: A Survey of Substrate Selectivity and Major Active Site Access Channels

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α‐hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25‐hydroxycholesterol (25‐HOChol), and other steroids such as 5α‐androstane‐3β,17β‐diol (anediol), and 5α‐androstene‐3β,17β‐diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site‐directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1. The results clearly identify the dominant access channels and critical residues responsible for ligand binding. Both binding free energy analysis and total interaction energy analysis are consistent with the experimental conclusion that 25‐HOChol is the best substrate. According to 20 ns MD simulations, the Phe cluster residues that lie above the active site, particularly Phe489, are proposed to merge the active site with the adjacent channel to the surface and accommodate substrate binding in a reasonable orientation. The investigation of CYP7B1–substrate binding modes provides detailed insights into the poorly understood structural features of human CYP7B1 at the atomic level, and will be valuable information for drug development and protein engineering.     

Distinct Stepwise Reduction of a Nickel?Nickel‐Bonded Compound Containing an α‐Diimine Ligand: From Perpendicular to Coaxial Structures

A nickel? nickel‐bonded complex, [{Ni(μ‐L^.?)}₂] ( 1 ; L=[(2,6‐iPr₂C₆H₃)NC(Me)]₂), was synthesized from reduction of the LNiBr₂ precursor by sodium metal. Further controllable reduction of 1 with 1.0, 2.0 and 3.0 equiv of Na, respectively, afforded the singly, doubly, and triply reduced compounds [Na(DME)₃] ? [{Ni(μ‐L^.?)}₂] ( 2 ; DME=1,2‐dimethoxyethane), [Na(Et₂O)]Na[(L^.?)Ni? NiL^2?] ( 3 ), and [Na(Et₂O)]₂Na[L^2?Ni? NiL^2?] ( 4 ). Here L represents the neutral ligand, L^.? denotes its radical monoanion, and L^2? is the dianion. All of the four compounds feature a short Ni? Ni bond from 2.2957(6) to 2.4649(8) Å. Interestingly, they display two different structures: the perpendicular ( 1 and 2 ) and the coaxial ( 3 and 4 ) structure, in which the metal? metal bond axis is perpendicular to or collinear with the axes of the α‐diimine ligands, respectively. The electronic structures, Ni? Ni bonding nature, and energetic comparisons of the two structure types were investigated by DFT computations.     

Nanoscale Control of Polyoxometalate Assembly: A {Mn8W4} Cluster within a {W36Si4Mn10} Cluster Showing a New Type of Isomerism

Two near isomeric clusters containing a novel {Mn₈W₄} Keggin cluster within a [W₃₆Mn₁₀Si₄O₁₃₆(OH)₄(H₂O)8]^24? cluster are reported: K₁₀Li₁₄ [W₃₆Si₄O₁₃₆Mn^II₁₀(OH)₄(H₂O)₈] ( 1 ) and K₁₀Li1_3.5Mn_0.25[W₃₆Si₄O₁₃₆Mn^II₁₀(OH)₄(H₂O)₈] ( 1′ ). Bulk characterization of the clusters has been carried out by single crystal X‐ray structure analysis, ICP‐MS, TGA, ESI‐MS, CV and SQUID‐magnetometer analysis. X‐ray analysis revealed that 1′ has eight positions within the central Keggin core that were disordered W/Mn whereas 1 contained no such disorder. This subtle difference is due to a differences is how the two clusters assemble and recrystallize from the same mother liquor and represents a new type of isomerism. The rapid recrystallization process was captured via digital microscopy and this uncovered two “intermediate” types of crystal which formed temporarily and provided nucleation sites for the final clusters to assemble. The intermediates were investigated by single crystal X‐ray analysis and revealed to be novel clusters K₄Li₂₂[W₃₆Si₄Mn₇O₁₃₆(H₂O)₈]?56 H₂O ( 2 ) and Mn₂K₈Li₁₄[W₃₆Si₄Mn₇O₁₃₆(H₂O)₈]?45 H₂O ( 3 ). The intermediate clusters contained different yet related building blocks to the final clusters which allowed for the postulation of a mechanism of assembly. This demonstrates a rare example where the use X‐ray crystallography directly facilitated understanding the means by which a POM assembled.     

Structure‐Based Optimization of the Terminal Tripeptide in Glycopeptide Dendrimer Inhibitors of Pseudomonas aeruginosa Biofilms Targeting LecA

The galactopeptide dendrimer GalAG2 ((β‐Gal‐OC₆H₄CO‐Lys‐Pro‐Leu)₄(Lys‐Phe‐Lys‐Ile)₂Lys‐His‐Ile‐NH₂) binds strongly to the Pseudomonas aeruginosa (PA) lectin LecA, and it inhibits PA biofilms, as well as disperses already established ones. By starting with the crystal structure of the terminal tripeptide moiety GalA‐KPL in complex with LecA, a computational mutagenesis study was carried out on the galactotripeptide to optimize the peptide–lectin interactions. 25 mutants were experimentally evaluated by a hemagglutination inhibition assay, 17 by isothermal titration calorimetry, and 3 by X‐ray crystallography. Two of these tripeptides, GalA‐KPY (dissociation constant (K_D)=2.7 μM ) and GalA‐KRL (K_D=2.7 μM ), are among the most potent monovalent LecA ligands reported to date. Dendrimers based on these tripeptide ligands showed improved PA biofilm inhibition and dispersal compared to those of GalAG2 , particularly G2KPY ((β‐Gal‐OC₆H₄CO‐Lys‐Pro‐Tyr)₄(Lys‐Phe‐Lys‐Ile)₂Lys‐His‐Ile‐NH₂). The possibility to retain and even improve the biofilm inhibition in several analogues of GalAG2 suggests that it should be possible to fine‐tune this dendrimer towards therapeutic use by adjusting the pharmacokinetic parameters in addition to the biofilm inhibition through amino acid substitutions.     

Longitudinal Relaxation Enhancement in 1H NMR Spectroscopy of Tissue Metabolites via Spectrally Selective Excitation

Nuclear magnetic resonance spectroscopy is governed by longitudinal (T₁) relaxation. For protein and nucleic acid experiments in solutions, it is well established that apparent T₁ values can be enhanced by selective excitation of targeted resonances. The present study explores such longitudinal relaxation enhancement (LRE) effects for molecules residing in biological tissues. The longitudinal relaxation recovery of tissue resonances positioned both down‐ and upfield of the water peak were measured by spectrally selective excitation/refocusing pulses, and compared with conventional water‐suppressed, broadband‐excited counterparts at 9.4 T. Marked LRE effects with up to threefold reductions in apparent T₁ values were observed as expected for resonances in the 6–9 ppm region; remarkably, statistically significant LRE effects were also found for several non‐exchanging metabolite resonances in the 1–4 ppm region, encompassing 30–50 % decreases in apparent T₁ values. These LRE effects suggest a novel means of increasing the sensitivity of tissue‐oriented experiments, and open new vistas to investigate the nature of interactions among metabolites, water and macromolecules at a molecular level.     

Towards the Core Structure of Strychnos Alkaloids Using Samarium Diiodide‐Induced Reactions of Indole Derivatives

This report describes the development of a first and second generation approach towards the synthesis of the ABCEG pentacyclic core structure of Strychnos alkaloids. First, we discuss a sequential approach applying a series of functional group transformations to prepare suitable precursors for cyclization reactions. These include attempts of samarium diiodide‐induced cyclizations or a Barbier‐type reaction of a transient lithium organyl, which successfully led to a tetracyclic key building block earlier used for the synthesis of strychnine. Secondly, we account our first steps towards the development of an atom‐economical samarium diiodide‐induced cascade reaction using “dimeric” indolyl ketones as cyclization precursors. In this context, we discuss plausible mechanisms for the samarium diiodide‐induced cascade reaction as well as transformations of the obtained tetracyclic dihydroindoline derivatives.     

Bioconjugatable Azo‐Based Dark‐Quencher Dyes: Synthesis and Application to Protease‐Activatable Far‐Red Fluorescent Probes

We describe the efficient synthesis and one‐step derivatization of novel, nonfluorescent azo dyes based on the Black Hole Quencher‐3 (BHQ‐3) scaffold. These dyes were equipped with various reactive and/or bioconjugatable groups (azido, α‐iodoacetyl, ketone, terminal alkyne, vicinal diol). The azido derivative was found to be highly reactive in the context of copper‐catalyzed azide–alkyne cycloaddition (CuAAC) reactions and allowed easy synthetic access to the first water‐soluble (sulfonated derivative) and aldehyde‐modified BHQ‐3 dyes, the direct preparation of which failed by means of conventional azo‐coupling reactions. The aldehyde‐ and α‐iodoacetyl‐containing fluorescence quenchers were readily conjugated to aminooxy‐ and cysteine‐containing peptides by the formation of a stable oxime or thioether linkage, respectively. Further fluorescent labeling of the resultant peptide conjugates with red‐ or far‐red‐emitting rhodamine or cyanine dyes through sequential and/or one‐pot bioconjugations, led to novel Förster resonance energy transfer (FRET) based probes suitable for the in vivo detection and imaging of urokinase plasminogen activator, a key protease in cancer invasion and metastasis.     

Catalytic Asymmetric Construction of Quaternary α‐Amino Acid Containing Pyrrolidines through 1,3‐Dipolar Cycloaddition of Azomethine Ylides to α‐Aminoacrylates

The first catalytic enantioselective 1,3‐dipolar cycloaddition of azomethine ylides to α‐aminoacrylate catalyzed by a AgOAc/ferrocenyl oxazolinylphosphine (FOXAP) system was developed, which exhibits excellent exo‐ and enantioselectivity (92–99 % ee). This process provides efficient access to useful 4‐aminopyrrolidine‐2,4‐dicarboxylic acid (APDC)‐like compounds containing a unique quaternary α‐amino acid unit.     

Controllable Syntheses of Porous Metal–Organic Frameworks: Encapsulation of LnIII Cations for Tunable Luminescence and Small Drug Molecules for Efficient Delivery

Two porous metal–organic frameworks (MOFs), [Zn₃(L)(H₂O)₂] ? 3 DMF ? 7 H₂O ( MOF‐1 ) and [(CH₃)₂NH₂]₆[Ni₃(L)₂(H₂O)₆] ? 3 DMF ? 15 H₂O ( MOF‐2 ), were synthesized solvothermally (H₆L=1,2,3,4,5,6‐hexakis(3‐carboxyphenyloxymethylene)benzene). In MOF ‐ 1 , neighboring Zn^II trimers are linked by the backbones of L ligands to form a fascinating 3D six‐connected framework with the point symbol (4¹².6³) (4¹².6³). In MOF‐2 , eight L ligands bridge six Ni^II atoms to generate a rhombic‐dodecahedral [Ni₆L₈] cage. Each cage is surrounded by eight adjacent ones through sharing of carboxylate groups to yield an unusual 3D porous framework. Encapsulation of Ln^III cations for tunable luminescence and small drug molecules for efficient delivery were investigated in detail for MOF‐1 .