Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states.

PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH+) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.

Incorporation of a bromine atom into DNA-related molecules changes their electronic properties.

To understand the mechanism underlying the high radio-sensitisation of living cells possessing brominated genomic DNA, X-ray photoelectron spectroscopy (XPS) using synchrotron X-rays with energies of 2000 or 2500 eV was used to study brominated and nonbrominated nucleobases, nucleosides and nucleotides. The bromine atom significantly reduced the energy gap between the valence and conduction states, although the core level states were not greatly affected. This finding was supported by quantum chemical calculation for the nucleobases and nucleosides. Our findings strongly indicate that the energy gaps between the valence and conduction levels of the molecules are significantly reduced by bromination. Furthermore, the brominated molecules are more likely to produce inelastic scattering low energy electrons upon exposure to 2000 or 3000 eV X-rays. This modification of electronic properties around the brominated group may both facilitate electron transfer to the brominated site in DNA and increase the probability of reaction with low energy electrons. These processes can induce DNA damage, presumably resulting in debromination of the uracil moiety and a subsequent cytotoxic effect.

Integrated Experimental and Computational Studies on the Organocatalytic Kinetic Resolution of ß-Unfunctionalized Primary Alcohols Using a Chiral 1,2-Diamine: The Importance of Noncovalent Interactions.

The enantioselective kinetic resolution of ß-unfunctionalized primary alcohols with benzoyl chloride was carried out in the presence of a catalytic amount of a novel chiral 1,2-diamine derived from (S)-proline. Several valuable chiral 2-substituted propan-1-ols were obtained with good enantioselectivities. Density functional theory calculations revealed that the noncovalent interaction, such as CH-π interaction, is crucial for the enantioselectivity of the resolution. This study was conducted through an interplay between experiment and computation.

Reaction Path Determination of Rhodium(I)-Catalyzed C-H Alkylation of N-8-Aminoquinolinyl Aromatic Amides with Maleimides.

The rhodium(I)-catalyzed reaction of N-8-aminoquinolinyl aromatic amides with maleimides results in C-H alkylation at the ortho position of the amide. The reaction path and formation of the alkylation product with density functional theory (DFT) calculations were done. The detailed computational study showed that the reaction proceeds in the following steps: (I) deprotonation of the NH amide proton, (II) oxidative addition of the ortho C-H bond, (III) migratory insertion of the maleimide, (IV) reductive elimination with the C-C bond formation, and (V) protonation. The energetic span model showed that the turnover frequency (TOF)-determining transition state (TDTS) is the oxidative addition, while the TOF-determining intermediate (TDI) is the formation of an Rh(I)-complex after N-H deprotonation. It was also found that the change in the oxidation number of the Rh catalyst is a key determinant of the reaction path.

Iridium(III)-Catalyzed Asymmetric Site-Selective Carbene C-H Insertion during Late-Stage Transformation.

C-H functionalization has recently received considerable attention because C-H functionalization during the late-stage transformation is a strong and useful tool for the modification of the bioactive compounds and the creation of new active molecules. Although a carbene transfer reaction can directly convert a C-H bond to the desired C-C bond in a stereoselective manner, its application in late-stage material transformation is limited. Here, we observed that the iridium-salen complex 6 exhibited efficient catalysis in asymmetric carbene C-H insertion reactions. Under optimized conditions, benzylic, allylic, and propargylic C-H bonds were converted to desired C-C bonds in an excellent stereoselective manner. Excellent regioselectivity was demonstrated in the reaction using not only simple substrate but also natural products, bearing multiple reaction sites. Moreover, based on the mechanistic studies, the iridium-catalyzed unique C-H insertion reaction involved rate-determining asynchronous concerted processes.

Calculation of CYP450 protein-ligand binding and dissociation free energy paths.

The function of an enzyme depends on its dynamic structure, and the catalytic mechanism has long been an active focus of research. The principle for interpreting protein selectivity and fidelity stems from optimization of the active site upon protein-substrate complexation, i.e., a lock-and-key configuration, on which most protein-substrate molecule binding recognition, and hence drug discovery, relies. Yet another thought has been to incorporate the protein folding interior tunnels for stereo- and regio-selectivity along the protein-substrate or protein-ligand/inhibitor binding process. Free energy calculations provide valuable information for molecular recognition and protein-ligand binding dynamics and kinetics. In this study, we focused on the kinetics of cytochrome P450 proteins (CYP450s) and the protein interior tunnel structure-dynamics relationship in terms of the substrate binding and leaving mechanism. A case in point is given by the prostaglandin H2 (PGH2) homologous isomerase of prostacyclin synthase. To calculate the reactant and product traversing the tunnels to and from the heme site, the free energy paths and tunnel potentials of mean force are constructed from steered molecular dynamics simulations and adaptive basing force umbrella sampling simulations. We explore the binding tunnels and critical residue lining characteristics for the ligand traverse and the underlying mechanism of CYP450 activity. Our theoretical analysis provides insights into the decisive role of the substrate tunnel binding process of the CYP450 mechanism and may be useful in drug design and protein engineering contexts.

Highly Modified Lanostane Triterpenes from the Wood-Rot Basidiomycete Ganoderma colossus: Comparative Chemical Investigations of Natural and Artificially Cultivated Fruiting Bodies and Mycelial Cultures.

The wood-rot basidiomycete Ganoderma colossus has been chemically investigated. Comparative analyses of the natural fruiting body, artificially cultivated fruiting bodies, and mycelial cultures resulted in the isolation, in total, of 13 new highly modified lanostanes, ganocolossusins A-H (1-8) and ganodermalactones T-X (9-13), together with 23 known compounds (14-36). There were significant overlaps of the same compounds among the three different states of the fungal materials. Ganocolossusin D (4) displayed the most potent antimalarial activity against Plasmodium falciparum K1 (multi-drug-resistant strain) with an IC50 value of 2.4 µM, while it was noncytotoxic to Vero cells at 50 µg/mL.

Theoretical investigations of Rh-catalyzed asymmetric 1,4-addition to enones using planar-chiral phosphine-olefin ligands.

Recently, planar-chiral phosphine-olefin ligands based on (η6 -arene)chromium(0) and (η5 -cyclopentadienyl)manganese(I), which are known as first- and second-generation, respectively, have been developed. These ligands were employed for Rh-catalyzed asymmetric 1,4-addition to enones. First-generation ligands involve high enantioselectivity for cyclic enones (>98% ee). Second-generation ligands involve high enantioselectivity for not only cyclic enones but also for acyclic enones (>98% ee). In this study, we have performed DFT calculations to investigate the origin of enantioselectivity. The theoretical values of enantioselectivities were found to be in good agreement with the experimental values obtained for a cyclic enone, 2-cyclopenten-1-one, using both the first- and second-generation ligands. Regarding an acyclic enone, 3-penten-2-one, it was found that the s-cis type decreases the enantioselectivity because the transition states in the s-cis type have a large steric repulsion. Energy decomposition analysis (EDA) and natural bond orbital (NBO) analysis indicate that it is important to study the orbital interactions in the transition states of the insertion step for the acyclic enone attacked from si-face with the second-generation ligand. © 2018 Wiley Periodicals, Inc.

π-π Stacking Interaction in an Oxidized CuII -Salen Complex with a Side-Chain Indole Ring: An Approach to the Function of the Tryptophan in the Active Site of Galactose Oxidase.

In order to gain new insights into the effect of the π-π stacking interaction of the indole ring with the CuII -phenoxyl radical as seen in the active form of galactose oxidase, we have prepared a CuII complex of a methoxy-substituted salen-type ligand, containing a pendent indole ring on the dinitrogen chelate backbone, and characterized its one-electron-oxidized forms. The X-ray crystal structures of the oxidized CuII complex exhibited the π-π stacking interaction of the indole ring mainly with one of the two phenolate moieties. The phenolate moiety in close contact with the indole moiety showed the characteristic phenoxyl radical structural features, indicating that the indole ring favors the π-π stacking interaction with the phenoxyl radical. The UV/Vis/NIR spectra of the oxidized CuII complex with the pendent indole ring was significantly different from those of the complex without the side-chain indole ring, and the absorption and CD spectra exhibited a solvent dependence, which is in line with the phenoxyl radical-indole stacking interaction in solution. The other physicochemical results and theoretical calculations strongly support that the indole ring, as an electron donor, stabilizes the phenoxyl radical by the π-π stacking interaction.

Design and characterization of a 2-(2'-hydroxyphenyl)benzimidazole-based Sr2+-selective fluorescent probe in organic and micellar solution systems.

A novel Sr2+ fluorescent probe, N-(2-hydroxy-3-(1H-benzimidazol-2-yl)-phenyl)-1-aza-18-crown-6-ether (BIC), was synthesized and its fluorescence properties, equilibria, and local structure in solution were studied in detail. The fluorescence intensity of BIC in DMSO was enhanced selectively upon addition of Sr2+ but not Na+, K+, Mg2+, Ca2+, and Ba2+. To employ this rather hydrophobic BIC probe in aqueous media, a sodium laurate (LaNa) micellar solution was used as a good solvent. The detection limit of said LaNa micelle-BIC system (2.02 µM) is lower than that of the H2O system (309 µM), but higher than that of the DMSO system (0.04 µM). Therefore, it is clear that the LaNa micelles have an effect on the detection of Sr2+ by BIC in aqueous solutions. Further structural studies by extended X-ray absorption fine structure and speciation analyses revealed that BIC undergoes complexation equilibria corresponding to the formation of [Sr(BIC)]+ species in all solution types. It was concluded that the changes in the Sr2+-BIC fluorescence in solution are attributed to the formation of such [Sr(BIC)]+ complexes.

Characterization of the one-electron oxidized Cu(II)-salen complexes with a side chain aromatic ring: the effect of the indole ring on the Cu(II)-phenoxyl radical species.

To gain insights into the role of the proximal indole ring in the redox-active metal center as seen in galactose oxidase, we prepared the Cu(II)-salen-type complexes having a pendent indol-3-ylmethyl (1), methyl (2) or benzyl (3) group substituted on the ethylenediamine moiety and investigated the structures and redox properties by various physicochemical methods and theoretical calculations. Neutral complexes 1, 2, and 3 showed no significant difference in the UV-Vis-NIR and EPR spectra. One-electron oxidation of 1, 2, and 3 by addition of 1 equiv. of thianthrenyl radical gave [1]SbCl 6 , [2]SbCl 6 , and [3]SbCl 6 , respectively, which could be assigned to relatively localized phenoxyl radical species. The cyclic and differential pulse voltammograms of [1]SbCl 6 showed two redox waves with a large separation between the first and second redox potentials compared with the separations observed for [2]SbCl 6 and [3]SbCl 6 . This suggests that [1]SbCl 6 is more stabilized than [2]SbCl 6 and [3]SbCl 6 . The NIR band of [1]SbCl 6 showed a larger blue shift than that of [2]SbCl 6 and [3]SbCl 6 . The EPR spectrum of [2]SbCl 6 exhibited an intense signal at the g value of 2 due to partial disproportionation to form the EPR active two-electron oxidized complex [2] 2+ , while the EPR intensity of [1]SbCl 6 was much weaker than that of [2]SbCl 6 . These results indicate that the pendent indole moiety stabilizes the Cu(II)-phenoxyl radical in [1]SbCl 6 most probably by stacking with the phenoxyl moiety, which is further supported by DFT calculations.

QM/MM Investigation for Protonation States in a Bilin Reductase PcyA-Biliverdin IXα Complex.

Herein we report quantum mechanical/molecular mechanical (QM/MM) studies to investigate the most probable protonation states of active site amino acids and bound substrate based on a recently reported neutron diffraction structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA) by Unno et al. This structure was considered to be bound in its initial state of biliverdin IXα (BV), which has the C-pyrrole ring in the deprotonated state. The protonation state of BV suggested by neutron and spectroscopic studies is a stable, two-electron reduced complex with a bound hydronium ion. Several ambiguities in the neutron structure were observed which prompted a further theoretical analysis of the structure. This structural investigation provides new understanding of the PcyA and BV protonation states not previously reported in the literature. Our calculations suggest that the hydronium ion (H3 O+ ) is energetically unfavorable, preferentially protonating the neighboring His88 residue and that the C-ring of BV is not protonated.

Combined Theoretical and Experimental Studies of Nickel-Catalyzed Cross-Coupling of Methoxyarenes with Arylboronic Esters via C-O Bond Cleavage.

Nickel(0)-catalyzed cross-coupling of methoxyarenes through C-O bond activation has been the subject of considerable research because of their favorable features compared with those of the cross-coupling of aryl halides, such as atom economy and efficiency. In 2008, we have reported nickel/PCy3-catalyzed cross-coupling of methoxyarenes with arylboronic esters in which the addition of a stoichiometric base such as CsF is essential for the reaction to proceed. Recently, we have also found that the scope of the substrate in the Suzuki-Miyaura-type cross-coupling of methoxyarenes can be greatly expanded by using 1,3-dicyclohexylimidazol-2-ylidene (ICy) as the ligand. Interestingly, a stoichiometric amount of external base is not required for the nickel/ICy-catalyzed cross-coupling. For the mechanism and origin of the effect of the external base to be elucidated, density functional theory calculations are conducted. In the nickel/PCy3-catalyzed reactions, the activation energy for the oxidative addition of the C(aryl)-OMe bond is too high to occur under the catalytic conditions. However, the oxidative addition process becomes energetically feasible when CsF and an arylboronic ester interact with a Ni(PCy3)2/methoxyarene fragment to form a quaternary complex. In the nickel/ICy-catalyzed reactions, the oxidative addition of the C(aryl)-OMe bond can proceed more easily without the aid of CsF because the nickel-ligand bonds are stronger and therefore stabilize the transition state. The subsequent transmetalation from an Ar-Ni-OMe intermediate is determined to proceed through a pathway with lower energies than those required for ß-hydrogen elimination. The overall driving force of the reaction is the reductive elimination to form the carbon-carbon bond.

Evaluation of dermal wound healing activity of synthetic peptide SVVYGLR.

SVVYGLR peptide (SV peptide) is a 7-amino-acid sequence with angiogenic properties that is derived from osteopontin in the extracellular matrix and promotes differentiation of fibroblasts to myofibroblast-like cells and the production of collagen type Ⅲ by cardiac fibroblasts. However, the effects of SV peptide on dermal cells and tissue are unknown. In this study, we evaluated the effects of this peptide in a rat model of dermal wound healing. The synthetic SV peptide was added to dermal fibroblasts or keratinocytes, and their cellular motility was evaluated. In an in vivo wound healing exeriment, male rats aged 8 weeks were randomly assigned to the SV peptide treatment, non-treated control, or phosphate-buffered saline (PBS) groups. Wound healing was assessed by its repair rate and histological features. Scratch assay and cell migration assays using the Chemotaxicell method showed that SV peptide significantly promoted the cell migration in both fibroblasts and keratinocytes. In contrast the proliferation potency of these cells was not affected by SV peptide. In the rat model, wound healing progressed faster in the SV peptide-treated group than in the control and PBS groups. The histopathological analyses showed that the SV peptide treatment stimulated the migration of fibroblasts to the wound area and increased the number of myofibroblasts. Immunohistochemical staining showed a marked increase of von Willebland factor-positive neomicrovessels in the SV peptide-treated group. In conclusion, SV peptide has a beneficial function to promote wound healing by stimulating granulation via stimulating angiogenesis, cell migration, and the myofibroblastic differentiation of fibroblasts.

Asymmetric Synthesis of ß-Lactams through Copper-Catalyzed Alkyne-Nitrone Coupling with a Prolinol-Phosphine Chiral Ligand.

Prolinol-phosphine chiral ligands enabled highly enantioselective copper-catalyzed intermolecular alkyne-nitrone coupling (Kinugasa reaction) to produce 1,3,4-trisubstituted chiral ß-lactams. A high level of enantiocontrol was achieved not only with aryl- or alkenylacetylenes but also with alkylacetylenes, which were important but unfavorable substrates in the previously reported protocols. Two-point hydrogen bonding between the chiral ligand and the nitrone oxyanion consisting of O-H⋅⋅⋅O and C(sp3 )-H⋅⋅⋅O hydrogen bonds is proposed.

Copper-Catalyzed γ-Selective and Stereospecific Allylic Cross-Coupling with Secondary Alkylboranes.

The scope of the copper-catalyzed coupling reactions between organoboron compounds and allylic phosphates is expanded significantly by employing triphenylphosphine as a ligand for copper, allowing the use of secondary alkylboron compounds. The reaction proceeds with complete γ-E-selectivity and preferential 1,3-syn stereoselectivity. The reaction of γ-silicon-substituted allylic phosphates affords enantioenriched α-stereogenic allylsilanes.

SVVYGLR motif of the thrombin-cleaved N-terminal osteopontin fragment enhances the synthesis of collagen type III in myocardial fibrosis.

Osteopontin (OPN) is involved in various physiological processes such as inflammatory and wound healing. However, little is known about the effects of OPN on these tissues. OPN is cleaved by thrombin, and cleavage of the N-terminal fragment exposes a SVVYGLR sequence on its C-terminus. In this study, we examined the effects of the thrombin-cleaved OPN fragments on fibroblasts and myocardial fibrosis, particularly the role of the SVVYGLR sequence. The recombinant thrombin-cleaved OPN fragments (N-terminal fragment [N-OPN], C-terminal fragment [C-OPN], and the N-terminal fragment lacking the SVVYGLR sequence [ΔSV N-OPN]) were added to fibroblasts, and the cellular motility, signal activity, and production of collagen were evaluated. A sustained-release gel containing an OPN fragment or SVVYGLR peptide was transplanted into a rat model of ischemic cardiomyopathy and the quantities and ratio of collagen type I (COL I) and type III (COL III) were estimated. N-OPN significantly promoted fibroblast migration. Smad signal activity, expression of smooth muscle actin (SMA), and the production of COL III were enhanced by N-OPN and SVVYGLR peptide. Conversely, ΔSV N-OPN and C-OPN had no effect. In vivo, the expression level of N-OPN was associated with COL III distribution, and the COL III/COL I ratio was significantly increased by the sustained-release gel containing N-OPN or SVVYGLR peptide. The cardiac function was also significantly improved by the N-OPN- or SVVYGLR peptide-released gel treatment. The N-terminal fragment of thrombin-cleaved OPN-induced Smad signal activation, SMA expression, and COL III production, and its SVVYGLR sequence influences this function.

Facile estimation of catalytic activity and selectivities in copolymerization of propylene oxide with carbon dioxide mediated by metal complexes with planar tetradentate ligand.

Mechanistic studies were conducted to estimate (1) catalytic activity for PPC, (2) PPC/CPC selectivity, and (3) PPC/PPO selectivity for the metal-catalyzed copolymerization of propylene oxide with carbon dioxide [PPC: poly(propylene carbonate); CPC = cyclic propylene carbonate; PPO: poly(propylene oxide)]. Density functional theory (DFT) studies demonstrated that the ΔG(crb) - ΔG(epx) value should be an effective indicator for the catalytic activities [ΔG(epx): dissociation energy of ethylene oxide from the epoxide-coordinating metal complex; ΔG(crb): dissociation energy of methyl carbonate from the metal-carbonate complex]. In addition, metal complexes with a subthreshold ΔG(epx) value were found to show low PPC/CPC selectivity. The PPC/PPO selectivity was related to the ΔG(alk) - ΔG(epx) value and steric environment around the metal center (ΔG(alk): dissociation energy of alkoxide ligand from the metal center). Based on the mechanistic studies, two metal complexes were designed and applied to the copolymerization to support validity of these indicators. The results presented here should be useful for brand-new catalyst candidates since these indicators can be easily calculated by DFT method without computing transition states.

Redox chemistry of nickel(II) complexes supported by a series of noninnocent ß-diketiminate ligands.

Nickel complexes of a series of ß-diketiminate ligands ((R)L(-), deprotonated form of 2-substituted N-[3-(phenylamino)allylidene]aniline derivatives (R)LH, R = Me, H, Br, CN, and NO2) have been synthesized and structurally characterized. One-electron oxidation of the neutral complexes [Ni(II)((R)L(-))2] by AgSbF6 or [Ru(III)(bpy)3](PF6)3 (bpy = 2,2'-bipyridine) gave the corresponding metastable cationic complexes, which exhibit an EPR spectrum due to a doublet species (S = 1/2) and a characteristic absorption band in near IR region ascribable to a ligand-to-ligand intervalence charge-transfer (LLIVCT) transition. DFT calculations have indicated that the divalent oxidation state of nickel ion (Ni(II)) is retained, whereas one of the ß-diketiminate ligands is oxidized to give formally a mixed-valence complex, [Ni(II)((R)L(-))((R)L(•))](+). Thus, the doublet spin state of the oxidized cationic complex can be explained by taking account of the antiferromagnetic interaction between the high-spin nickel(II) ion (S = 1) and the organic radical (S = 1/2) of supporting ligand. A single-crystal structure of one of the cationic complexes (R = H) has been successfully determined to show that both ligands in the cationic complex are structurally equivalent. On the basis of theoretical analysis of the LLIVCT band and DFT calculations as well as the crystal structure, the mixed-valence complexes have been assigned to Robin-Day class III species, where the radical spin is equally delocalized between the two ligands to give the cationic complex, which is best described as [Ni(II)((R)L(0.5•-))2](+). One-electron reduction of the neutral complexes with decamethylcobaltocene gave the anionic complexes when the ligand has the electron-withdrawing substituent (R = CN, NO2, Br). The generated anionic complexes exhibited EPR spectra due to a doublet species (S = 1/2) but showed no LLIVCT band in the near-IR region. Thus, the reduced complexes are best described as the d(9) nickel(I) complexes supported by two anionic ß-diketiminate ligands, [Ni(I)((R)L(-))2](-). This conclusion was also supported by DFT calculations. Substituent effects on the electronic structures of the three oxidation states (neutral, cationic, and anionic) of the complexes are systematically evaluated on the basis of DFT calculations.

FGF9, a Potent Mitogen, Is a New Ligand for Integrin αvß3, and the FGF9 Mutant Defective in Integrin Binding Acts as an Antagonist.

FGF9 is a potent mitogen and survival factor, but FGF9 protein levels are generally low and restricted to a few adult organs. Aberrant expression of FGF9 usually results in cancer. However, the mechanism of FGF9 action has not been fully established. Previous studies showed that FGF1 and FGF2 directly bind to integrin αvß3, and this interaction is critical for signaling functions (FGF-integrin crosstalk). FGF1 and FGF2 mutants defective in integrin binding were defective in signaling, whereas the mutants still bound to FGFR suppressed angiogenesis and tumor growth, indicating that they act as antagonists. We hypothesize that FGF9 requires direct integrin binding for signaling. Here, we show that docking simulation of the interaction between FGF9 and αvß3 predicted that FGF9 binds to the classical ligand-binding site of αvß3. We show that FGF9 bound to integrin αvß3 and generated FGF9 mutants in the predicted integrin-binding interface. An FGF9 mutant (R108E) was defective in integrin binding, activating FRS2α and ERK1/2, inducing DNA synthesis, cancer cell migration, and invasion in vitro. R108E suppressed DNA synthesis and activation of FRS2α and ERK1/2 induced by WT FGF9 (dominant-negative effect). These findings indicate that FGF9 requires direct integrin binding for signaling and that R108E has potential as an antagonist to FGF9 signaling.