Discovery and Biosynthesis of Cihanmycins Reveal Cytochrome P450-Catalyzed Intramolecular C-O Phenol Coupling Reactions.

Cinnamoyl-containing nonribosomal peptides (CCNPs) constitute a unique family of natural products. The enzyme mechanism for the biaryl phenol coupling reaction of the bicyclic CCNPs remains unclear. Herein, we report the discovery of two new arabinofuranosylated bicyclic CCNPs cihanmycins (CHMs) A (1) and B (2) from Amycolatopsis cihanbeyliensis DSM 45679 and the identification of the CHM biosynthetic gene cluster (cih BGC) by heterologous expression in Streptomyces lividans SBT18 to afford CHMs C (3) and D (4). The structure of 1 was confirmed by X-ray diffraction analysis. Three cytochrome P450 enzyme (CYP)-encoding genes cih26, cih32, and cih33 were individually inactivated in the heterologous host to produce CHMs E (5), F (6), and G (7), respectively. The structures of 5 and 6 indicated that Cih26 was responsible for the hydroxylation and epoxidation of the cinnamoyl moiety, and Cih32 should catalyze the ß-hydroxylation of three amino acid residues. Cih33 and its homologues DmlH and EpcH were biochemically verified to convert CHM G (7) with a monocyclic structure to a bicyclic skeleton of CHM C (3) through an intramolecular C-O phenol coupling reaction. The substrate 7-bound crystal structure of DmlH not only established the structure of 7, which was difficult for NMR analysis for displaying anomalous splitting signals, but also provided the binding mode of macrocyclic peptides recognized by these intramolecular C-O coupling CYPs. In addition, computational studies revealed a water-mediated diradical mechanism for the C-O phenol coupling reaction. These findings have shed important mechanistic insights into the CYP-catalyzed phenol coupling reactions.

Linkage conversions in single-crystalline covalent organic frameworks.

Single-crystal X-ray diffraction is a powerful characterization technique that enables the determination of atomic arrangements in crystalline materials. Growing or retaining large single crystals amenable to it has, however, remained challenging with covalent organic frameworks (COFs), especially suffering from post-synthetic modifications. Here we show the synthesis of a flexible COF with interpenetrated qtz topology by polymerization of tetra(phenyl)bimesityl-based tetraaldehyde and tetraamine building blocks. The material is shown to be flexible through its large, anisotropic positive thermal expansion along the c axis (αc = +491 × 10-6 K-1), as well as through a structural transformation on the removal of solvent molecules from its pores. The as-synthesized and desolvated materials undergo single-crystal-to-single-crystal transformation by reduction and oxidation of its imine linkages to amine and amide ones, respectively. These redox-induced linkage conversions endow the resulting COFs with improved stability towards strong acid; loading of phosphoric acid leads to anhydrous proton conductivity up to ca. 6.0 × 10-2 S cm-1.

Molecular Vises for Precisely Positioning Ligands near Catalytic Metal Centers in Metal-Organic Frameworks.

We report the construction of a molecular vise by pairing a tritopic phenylphosphorus(III) linker and a monotopic linker in opposite positions within a metal-organic framework. The angle between these linkers at metal sites is fixed upon changing the functionality in the monotopic linker, while the distance between them is precisely tuned. This distance within the molecular vise is accurately measured by 1H-31P solid-state nuclear magnetic resonance spectroscopy. This unveils the impact of the distance on catalytic performance without interference from electrostatic effects or changes in the angle of the ligand, which is unprecedented in classic organometallic complexes.

Different Silver Nanoparticles in One Crystal: Ag210 (i PrPhS)71 (Ph3 P)5 Cl and Ag211 (i PrPhS)71 (Ph3 P)6 Cl.

Two pure silver nanoparticles (Ag210 (i PrPhS)71 (Ph3 P)5 Cl and Ag211 (i PrPhS)71 (Ph3 P)6 Cl labeled as SD/Ag210 and SD/Ag211 (SD=SunDi), were found to co-crystallize in forming compound 1. Single-crystal X-ray diffraction (SCXRD) revealed that they differ by only one Ag(PPh3 ). Their four-shell nanoparticles consist of three pure Ag metal shells (Ag19 @Ag52 @Ag45 ) shielded by a silver-organic Ag89 (i PrPhS)71 Cl[Ag(Ph3 P)]n outermost shell. The number (n) of Ag(Ph3 P) is five for SD/Ag210 and six for SD/Ag211. The pseudo-fivefold symmetric Ag nanoparticles exhibit surface plasmon absorption similar to a true metallic state but at the nanoscale. This work exemplifies the important effects of phosphine in stabilizing large silver nanoparticles; and offers a platform to investigate the origin of differences in nanoscale metal materials, even differing by only one metal atom; it also sheds light on the regioselective binding of auxiliary Ph3 P on the surface of silver nanoparticles.

Refolding and kinetic characterization of the phosphodiesterase-8A catalytic domain.

Cyclic nucleotide phosphodiesterase-8 (PDE8) hydrolyzes the second messenger cAMP and is involved in many biological processes such as testosterone production. Although the bacterial and mammalian expression systems have been extensively tried, production of large quantity of soluble and active PDE8 remains to be a major hurdle for pharmacological and structural studies. Reported here is a detailed protocol of refolding and purification of large quantity of the PDE8A1 catalytic domain (residues 480-820) and kinetic characterization of the refolded protein. This protocol yielded about 8 mg of the PDE8A catalytic domain from 2l Escherichia coli culture, which has at least 40-fold higher activity than those reported in literature. The PDE8A1 catalytic domain has k(cat) of 4.0 s(-1) for Mn(2+) and 2.9s(-1) for Mg(2+), and the K(M) values of 1-1.8 microM. In addition, the PDE8A1 (205-820) fragment that contains both PAS and catalytic domains was expressed in E. coli and refolded. This PDE8A1 (205-820) fragment has k(cat) of 1.1 s(-1) and K(M) of 0.28 microM, but aggregated at high concentration. The K(M) of PDE8A1 (205-820) is 2- to 7-fold higher than the K(M) values of 40-150 nM for the full-length PDE8s in literature, but about 6-fold lower than that of the catalytic domain. Thus, the K(M) difference likely implies an allosteric regulation of the PDE8A activity by its PAS domain.

Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity.

Cyclic nucleotide phosphodiesterase-8 (PDE8) is a family of cAMP-specific enzymes and plays important roles in many biological processes, including T-cell activation, testosterone production, adrenocortical hyperplasia, and thyroid function. However, no PDE8 selective inhibitors are available for trial treatment of human diseases. Here we report kinetic properties of the highly active PDE8A1 catalytic domain prepared from refolding and its crystal structures in the unliganded and 3-isobutyl-1-methylxanthine (IBMX) bound forms at 1.9 and 2.1 A resolutions, respectively. The PDE8A1 catalytic domain has a K(M) of 1.8 microM, V(max) of 6.1 micromol/min/mg, a k(cat) of 4.0 s(-1) for cAMP, and a K(M) of 1.6 mM, V(max) of 2.5 micromol/min/mg, a k(cat) of 1.6 s(-1) for cGMP, thus indicating that the substrate specificity of PDE8 is dominated by K(M). The structure of the PDE8A1 catalytic domain has similar topology as those of other PDE families but contains two extra helices around Asn685-Thr710. Since this fragment is distant from the active site of the enzyme, its impact on the catalysis is unclear. The PDE8A1 catalytic domain is insensitive to the IBMX inhibition (IC(50) = 700 microM). The unfavorable interaction of IBMX in the PDE8A1-IBMX structure suggests an important role of Tyr748 in the inhibitor binding. Indeed, the mutation of Tyr748 to phenylalanine increases the PDE8A1 sensitivity to several nonselective or family selective PDE inhibitors. Thus, the structural and mutagenesis studies provide not only insight into the enzymatic properties but also guidelines for design of PDE8 selective inhibitors.

Crystal structure of the Leishmania major phosphodiesterase LmjPDEB1 and insight into the design of the parasite-selective inhibitors.

Human leishmaniasis is a major public health problem in many countries, but chemotherapy is in an unsatisfactory state. Leishmania major phosphodiesterases (LmjPDEs) have been shown to play important roles in cell proliferation and apoptosis of the parasite. Thus LmjPDE inhibitors may potentially represent a novel class of drugs for the treatment of leishmaniasis. Reported here are the kinetic characterization of the LmjPDEB1 catalytic domain and its crystal structure as a complex with 3-isobutyl-1-methylxanthine (IBMX) at 1.55 A resolution. The structure of LmjPDEB1 is similar to that of human PDEs. IBMX stacks against the conserved phenylalanine and forms a hydrogen bond with the invariant glutamine, in a pattern common to most inhibitors bound to human PDEs. However, an extensive structural comparison reveals subtle, but significant differences between the active sites of LmjPDEB1 and human PDEs. In addition, a pocket next to the inhibitor binding site is found to be unique to LmjPDEB1. This pocket is isolated by two gating residues in human PDE families, but constitutes a natural expansion of the inhibitor binding pocket in LmjPDEB1. The structure particularity might be useful for the development of parasite-selective inhibitors for the treatment of leishmaniasis.

Crystal structure of a cyclomaltoheptaose-4-hydroxybiphenyl inclusion complex.

The crystal structure of the inclusion complex of cyclomaltoheptaose (beta-cyclodextrin) with 4-hydroxybiphenyl was determined by single-crystal X-ray diffraction at 150K. The complex contains two cyclomaltoheptaose molecules, two 4-hydroxybiphenyl molecules, one ethanol molecule and fifteen water molecules in the asymmetric unit, and could be formulated as [2(C(42)H(70)O(35)).2(C(12)H(10)O).(C(2)H(6)O).15(H(2)O)]. It crystallized in the triclinic space group P1 with unit cell constants a=15.257(3), b=15.564(3), c=15.592(2)A, alpha=104.485(15) degrees , beta=101.066(14) degrees , gamma=104.330(17) degrees , V=3,343.6(10)A(3). In the crystal lattice, two beta-cyclodextrins form a head-to-head dimer jointed through hydrogen bonds. Two 4-hydroxybiphenyls were included in the dimer cavity with their hydroxyl groups protruding from two primary hydroxyl sides of the cyclodextrin molecules. The guest 4-hydroxybiphenyl molecules linked into a chain via a combination of an O-Hcdots, three dots, centeredO hydrogen bond and face-to-face pi-pi stacking of the phenyl rings. The crystal structure supports the calculation results indicating that the 2:2 inclusion complex formed by beta-cyclodextrin and 4-hydroxybiphenyl is the energetically favored structure.