Characterization of Radical SAM Adenosylhopane Synthase,HpnH, which Catalyzes the 5′‐Deoxyadenosyl Radical Addition to Diploptene in the Biosynthesis of C35 Bacteriohopanepolyols

Adenosylhopane is a crucial intermediate in the biosynthesis of bacteriohopanepolyols, which are widespread prokaryotic membrane lipids. Herein, it is demonstrated that reconstituted HpnH, a putative radical S‐adenosyl‐l ‐methionine (SAM) enzyme, commonly encoded in the hopanoid biosynthetic gene cluster, converts diploptene into adenosylhopane in the presence of SAM, flavodoxin, flavodoxin reductase, and NADPH. NMR spectra of the enzymatic reaction product were identical to those of synthetic (22R)‐adenosylhopane, indicating that HpnH catalyzes stereoselective C?C formation between C29 of diploptene and C5′ of 5′‐deoxyadenosine. Further, the HpnH reaction in D₂O‐containing buffer revealed that a D atom was incorporated at the C22 position of adenosylhopane. Based on these results, we propose a radical addition reaction mechanism catalyzed by HpnH for the formation of the C₃₅ bacteriohopane skeleton.     

Facile Chemoenzymatic Strategies for the Synthesis and Utilization of S‐Adenosyl‐L‐Methionine Analogues

A chemoenzymatic platform for the synthesis of S‐adenosyl‐L ‐methionine (SAM) analogues compatible with downstream SAM‐utilizing enzymes is reported. Forty‐four non‐native S/Se‐alkylated Met analogues were synthesized and applied to probing the substrate specificity of five diverse methionine adenosyltransferases (MATs). Human MAT II was among the most permissive of the MATs analyzed and enabled the chemoenzymatic synthesis of 29 non‐native SAM analogues. As a proof of concept for the feasibility of natural product “alkylrandomization”, a small set of differentially‐alkylated indolocarbazole analogues was generated by using a coupled hMAT2–RebM system (RebM is the sugar C4′‐O‐methyltransferase that is involved in rebeccamycin biosynthesis). The ability to couple SAM synthesis and utilization in a single vessel circumvents issues associated with the rapid decomposition of SAM analogues and thereby opens the door for the further interrogation of a wide range of SAM utilizing enzymes.     

7‐Cyclopropyl‐2′‐deoxytubercidin: a carbocyclic side‐chain derivative of 7‐deaza‐2′‐deoxyadenosine

The title compound {systematic name: 4‐amino‐5‐cyclopropyl‐7‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐7H‐pyrrolo[2,3‐d]pyrimidine}, C₁₄H₁₈N₄O₃, exhibits an anti glycosylic bond conformation, with the torsion angle χ = −108.7 (2)°. The furanose group shows a twisted C1′‐exo sugar pucker (S‐type), with P = 120.0 (2)° and τ_m = 40.4 (1)°. The orientation of the exocyclic C4′—C5′ bond is ‐ap (trans), with the torsion angle γ = −167.1 (2)°. The cyclopropyl substituent points away from the nucleobase (anti orientation). Within the three‐dimensional extended crystal structure, the individual molecules are stacked and arranged into layers, which are highly ordered and stabilized by hydrogen bonding. The O atom of the exocyclic 5′‐hydroxy group of the sugar residue acts as an acceptor, forming a bifurcated hydrogen bond to the amino groups of two different neighbouring molecules. By this means, four neighbouring molecules form a rhomboidal arrangement of two bifurcated hydrogen bonds involving two amino groups and two O5′ atoms of the sugar residues.     

Quantum chemistry studies of adenosine 2503 methylation by S‐adenosylmethionine‐dependent enzymes

Ribosome methylation is important for life processes and is mainly catalyzed by radical S‐Adenosylmethionine (SAM) enzymes. Two SAM molecules serve as the cofactor by providing the 5 ′‐deoxyadenosyl radical for substrate activation and the methyl. Recently, Booker and coworkers (Science 2011, 332, 604) proposed an alternative mechanism for a pair of radical SAM enzymes, RlmN and Cfr, which respectively methylate the C2 and C8 of adenosine 2503. Their deuterium labeling experiments reveal that methyl group does not transfer directly from SAM to adenosine, instead it passes to Cys³⁵⁵ first, then onto adenosine. In this article, this new reaction mechanism is studied using density functional theory with B3LYP hybrid functional. The reaction system is simulated using small model compounds in the gas phase, and the protein environment is approximated using polarizable continuum model. The structures of the transition states and the intermediates are identified, and their free energies are calculated. The activation barriers indicate that the proposed reaction mechanism is plausible. The formation of a disulfide bond is found to be the rate‐limiting step. © 2012 Wiley Periodicals, Inc.     

The Catalytic Mechanism of the Class C Radical S‐Adenosylmethionine Methyltransferase NosN

S ‐Adenosylmethionine (SAM) is one of the most common co‐substrates in enzyme‐catalyzed methylation reactions. Most SAM‐dependent reactions proceed through an S_N2 mechanism, whereas a subset of them involves radical intermediates for methylating non‐nucleophilic substrates. Herein, we report the characterization and mechanistic investigation of NosN, a class C radical SAM methyltransferase involved in the biosynthesis of the thiopeptide antibiotic nosiheptide. We show that, in contrast to all known SAM‐dependent methyltransferases, NosN does not produce S ‐adenosylhomocysteine (SAH) as a co‐product. Instead, NosN converts SAM into 5′‐methylthioadenosine as a direct methyl donor, employing a radical‐based mechanism for methylation and releasing 5′‐thioadenosine as a co‐product. A series of biochemical and computational studies allowed us to propose a comprehensive mechanism for NosN catalysis, which represents a new paradigm for enzyme‐catalyzed methylation reactions.     

2′‐Deoxy‐5‐propynyluridine: a nucleoside with two conformations in the asymmetric unit

The title compound, 1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐(prop‐1‐ynyl)pyrimidin‐2,4(1H,3H)‐dione, C₁₂H₁₄N₂O₅, shows two conformations in the crystalline state: conformer 1 adopts a C2′‐endo (close to ²E; S‐type) sugar pucker and an anti nucleobase orientation [χ = −134.04 (19)°], while conformer 2 shows an S sugar pucker (twisted C2′‐endo–C3′‐exo), which is accompanied by a different anti base orientation [χ = −162.79 (17)°]. Both molecules show a +sc (gauche, gauche) conformation at the exocyclic C4′—C5′ bond and a coplanar orientation of the propynyl group with respect to the pyrimidine ring. The extended structure is a three‐dimensional hydrogen‐bond network involving intermolecular N—H...O and O—H...O hydrogen bonds. Only O atoms function as H‐atom acceptor sites.     

7‐Iodo‐5‐aza‐7‐deazaguanine ribonucleoside: crystal structure,physical properties,base‐pair stability and functionalization

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> ( 1 ). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H…O and N—H…O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.     

Copper‐Complex‐Catalyzed Asymmetric Aerobic Oxidative Cross‐Coupling of 2‐Naphthols: Enantioselective Synthesis of 3,3′‐Substituted C1‐Symmetric BINOLs

A novel chiral 1,5‐N,N‐bidentate ligand based on a spirocyclic pyrrolidine oxazoline backbone was designed and prepared, and it coordinates CuBr in situ to form an unprecedented catalyst that enables efficient oxidative cross‐coupling of 2‐naphthols. Air serves as an external oxidant and generates a series of C₁‐symmetric chiral BINOL derivatives with high enantioselectivity (up to 99 % ee) and good yield (up to 87 %). This approach is tolerant of a broader substrates scope, particularly substrates bearing various 3‐ and 3′‐substituents. A preliminary investigation using one of the obtained C₁‐symmetric BINOL products was used as an organocatalyst, exhibiting better enantioselectivity than the previously reported organocatalyst, for the asymmetric α‐alkylation of amino esters.     

Phosphine‐Catalyzed Activation of Vinylcyclopropanes: Rearrangement of Vinylcyclopropylketones to Cycloheptenones

We report a phosphine‐catalyzed activation of electron‐deficient vinylcyclopropanes (VCPs) to generate an ambident C₅ synthon that is poised to undergo consecutive reactions. The utility of the activation is demonstrated in a phosphine‐catalyzed rearrangement of vinylcyclopropylketones to cycloheptenones in good yields with a broad substrate scope. Mechanistic investigations support a stepwise process comprising homoconjugate addition, water‐assisted proton transfer, and 7‐endo‐trig S_N2′ ring closure.     

Synthesis of All‐Carbon Disubstituted Bicyclo[1.1.1]pentanes by Iron‐Catalyzed Kumada Cross‐Coupling

1,3‐Disubstituted bicyclo[1.1.1]pentanes (BCPs) are important motifs in drug design as surrogates for p‐substituted arenes and alkynes. Access to all‐carbon disubstituted BCPs via cross‐coupling has to date been limited to use of the BCP as the organometallic component, which restricts scope due to the harsh conditions typically required for the synthesis of metallated BCPs. Here we report a general method to access 1,3‐C‐disubstituted BCPs from 1‐iodo‐bicyclo[1.1.1]pentanes (iodo‐BCPs) by direct iron‐catalyzed cross‐coupling with aryl and heteroaryl Grignard reagents. This chemistry represents the first general use of iodo‐BCPs as electrophiles in cross‐coupling, and the first Kumada coupling of tertiary iodides. Benefiting from short reaction times, mild conditions, and broad scope of the coupling partners, it enables the synthesis of a wide range of 1,3‐C‐disubstituted BCPs including various drug analogues.     

The 2‐Cyano‐2,2‐dimethylethanimine‐N‐oxymethyl Group for the 2′‐Hydroxyl Protection of Ribonucleosides in the Solid‐Phase Synthesis of RNA Sequences

The reaction of 2‐cyano‐2‐methyl propanal with 2′‐O‐aminooxymethylribonucleosides leads to stable and yet reversible 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl)ribonucleosides. Following N‐protection of the nucleobases, 5′‐dimethoxytritylation and 3′‐phosphitylation, the resulting 2′‐protected ribonucleoside phosphoramidite monomers are employed in the solid‐phase synthesis of three chimeric RNA sequences, each differing in their ratios of purine/pyrimidine. When the activation of phosphoramidite monomers is performed in the presence of 5‐benzylthio‐1H‐tetrazole, coupling efficiencies averaging 99 % are obtained within 180 s. Upon completion of the RNA‐chain assemblies, removal of the nucleobase and phosphate protecting groups and release of the sequences from the solid support are carried out under standard basic conditions, whereas the cleavage of 2′‐O‐(2‐cyano‐2,2‐dimethylethanimine‐N‐oxymethyl) protective groups is effected (without releasing RNA alkylating side‐products) by treatment with tetra‐n‐butylammonium fluoride (0.5 m) in dry DMSO over a period of 24–48 h at 55 °C. Characterization of the fully deprotected RNA sequences by polyacrylamide gel electrophoresis (PAGE), enzymatic hydrolysis, and matrix‐assisted laser desorption/ionization (MALDI) mass spectrometry confirmed the identity and quality of these sequences. Thus, the use of 2′‐O‐aminooxymethylribonucleosides in the design of new 2′‐hydroxyl protecting groups is a powerful approach to the development of a straightforward, efficient, and cost‐effective method for the chemical synthesis of high‐quality RNA sequences in the framework of RNA interference applications.     

7‐De­aza‐2′‐deoxy‐7‐propynyl­guanosine

The title compound, C₁₄H₁₆N₄O₄, adopts the anti conformation at the gly­cosylic bond [χ−117.1 (5)°]. The sugar pucker of the 2′‐deoxy­ribo­furan­osyl moiety is C2′‐endo–C3′‐exo, ²T₃ (S‐type). The orientation of the exocyclic C4′—C5′ bond is +sc (gauche). The propynyl group is linear and coplanar with the nucleobase moiety. The structure of the compound is stabilized by several hydrogen bonds (N—H⋯O and O—H⋯O), leading to the formation of a multi‐layered network. The nucleobases, as well as the propynyl groups, are stacked. This stacking might cause the extraordinary stability of DNA duplexes containing this compound.     

Novel Compounds with a Viologen Skeleton and N‐Heterocycles on the Peripheries: Electrochemical and Spectroscopic Properties

The present article deals with novel compounds comprising a redox‐active group as core and a nucleobase in the peripheries, linked covalently via a spacer. The new derivatives 1,1′,1″‐(benzene‐1,3,5‐triyltrimethanediyl)tris{1′‐[3‐(3,4‐dihydro‐5‐methyl‐2,4‐dioxopyrimidin‐1(2H)‐yl)propyl]‐4,4′‐bipyridinium} hexafluorophosphate ( 1 ), 1,1′,1″‐(benzene‐1,3,5‐triyltrimethanediyl)tris{1′‐[2‐(4‐chloro‐7H‐pyrrolo[2,3‐d]pyrimidine‐7‐yl)ethyl]‐4,4′‐bipyridinium} hexachloride ( 2a ) 1

1 The numbering of the pyrrolo[2,3‐d]pyrimidine system follows the IUPAC rules and is different from that of the purine ring system.

, and 1,1′,1″‐(benzene‐1,3,5‐triyltrimethanediyl)tris{1′‐[2‐(2‐amino‐4‐chloro‐7H‐pyrrolo[2,3‐d]pyrimidine‐7‐yl)ethyl]‐4,4′‐bipyridinium} hexabromide ( 2b )¹) were synthesized by nucleobase‐anion alkylation and linked to the 4,4′‐bipyridinium core. UV and CV analyses of these compounds were performed and revealed significantly different properties.     

8‐Aza‐7‐deaza‐7‐propynyladenosine methanol solvate

In the title compound, 4‐amino‐3‐propynyl‐1‐(β‐d ‐ribofur­anosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine methanol solvate, C₁₃H₁₅N₅O₄·CH₃OH, the torsion angle of the N‐glycosylic bond is between anti and high‐anti [χ = −101.8 (5)°]. The ribofuranose moiety adopts the C3′‐endo (³T₂) sugar conformation (N‐type) and the conformation at the exocyclic C—C bond is +sc (gauche, gauche). The propynyl group is out of the plane of the nucleobase and is bent. The compound forms a three‐dimensional network which is stabilized by several hydrogen bonds (O—H·O and O—H·N). The nucleobases are stacked head‐to‐tail. The methanol solvent mol­ecule forms hydrogen bonds with both the nucleobase and the sugar moiety.     

A locked derivative of 8‐aza‐7‐deazaadenosine

The title compound [systematic name: (1S,3S,4R,7S)‐3‐(4‐amino‐1H‐pyrazolo[3,4‐d]pyrimidin‐1‐yl)‐1‐hydroxymethyl‐2,5‐dioxabicyclo[2.2.1]heptan‐7‐ol], C₁₁H₁₃N₅O₄, belongs to a family of nucleosides with modifications in both the sugar and nucleobase moieties: these modifications are known to increase the thermodynamic stability of DNA and RNA duplexes. There are two symmetry‐independent molecules in the asymmetric unit that differ significantly in conformation, and both exhibit a high‐anti conformation about the N‐glycosidic bond, with χ torsion angles of −85.4 (3) and −87.4 (3)°. The sugar C atom attached to the nucleobase N atom is −0.201 (4) and 0.209 (4) Å from the 8‐aza‐7‐deazaadenine skeleton plane in the two molecules. The molecules are assembled into layers via hydrogen bonds and π–π stacking interactions between the modified nucleobases.     

Four N7‐alkoxybenzyl‐substituted 4,5,6,7‐tetrahydro‐1H‐pyrazolo[3,4‐b]pyridine‐5‐spiro‐1′‐cyclohexane‐2′,6′‐diones: hydrogen‐bonded supramolecular structures in zero,one, two or three dimensions

3‐tert‐Butyl‐7‐(4‐methoxybenzyl)‐4′,4′‐dimethyl‐1‐phenyl‐4,5,6,7‐tetrahydro‐1H‐pyrazolo[3,4‐b]pyridine‐5‐spiro‐1′‐cyclohexane‐2′,6′‐dione, C₃₁H₃₇N₃O₃, (I), 3‐tert‐butyl‐7‐(2,3‐dimethoxybenzyl)‐4′,4′‐dimethyl‐1‐phenyl‐4,5,6,7‐tetrahydro‐1H‐pyrazolo[3,4‐b]pyridine‐5‐spiro‐1′‐cyclohexane‐2′,6′‐dione, C₃₂H₃₉N₃O₄, (II), 3‐tert‐butyl‐4′,4′‐dimethyl‐7‐(3,4‐methylenedioxybenzyl)‐1‐phenyl‐4,5,6,7‐tetrahydro‐1H‐pyrazolo[3,4‐b]pyridine‐5‐spiro‐1′‐cyclohexane‐2′,6′‐dione, C₃₁H₃₅N₃O₄, (III), and 3‐tert‐butyl‐4′,4′‐dimethyl‐1‐phenyl‐7‐(3,4,5‐trimethoxybenzyl)‐4,5,6,7‐tetrahydro‐1H‐pyrazolo[3,4‐b]pyridine‐5‐spiro‐1′‐cyclohexane‐2′,6′‐dione ethanol 0.67‐solvate, C₃₃H₄₁N₃O₅·0.67C₂H₆O, (IV), all contain reduced pyridine rings having half‐chair conformations. The molecules of (I) and (II) are linked into centrosymmetric dimers and simple chains, respectively, by C—H...O hydrogen bonds, augmented only in (I) by a C—H...π hydrogen bond. The molecules of (III) are linked by a combination of C—H...O and C—H...π hydrogen bonds into a chain of edge‐fused centrosymmetric rings, further linked by weak hydrogen bonds into supramolecular arrays in two or three dimensions. The heterocyclic molecules in (IV) are linked by two independent C—H...O hydrogen bonds into sheets, from which the partial‐occupancy ethanol molecules are pendent. The significance of this study lies in its finding of a very wide range of supramolecular aggregation modes dependent on rather modest changes in the peripheral substituents remote from the main hydrogen‐bond acceptor sites.     

Silica Hybrid Containing （ R ）-2, 2＇-Binaphtho-20-crown-6 Moieties via the Sol-Gel Process

(R)-6,6‘-Bis(triethoxysilylethen-2-yl)-2,2-‘binaphtho-20-crown-6(precursor,R-2) derived form(R)-2,2-BINOL derivative was synthesized by Pd-catelyzed Heck reaction of (R)-6-6‘-dibromo-2,2‘-binaphtoh-20-crown-6(R-1) intermediate with vinyltriethoxysilane. The hydrolysis and polycondensatlon ofthe precursor gave rise to the corresponding xerogei. Both pre cursor and xerogei were analysed by NMR, FT-IR, UV, CD spectra, fluorescent spectroscopy, polarimetry and elemental analysis. The precursor and xerogei can emit strong blue fluorescenee and are expected to have the potential appficatiou inthe separation of chiral molecules as fluorescent sensor. The precursor exhibits strong Cotton effect in its circular dichroism (CD) spectrum indicating that it is a highly rigid structure.     

Utility of Pyridine‐2(1H)‐thiones in the Synthesis of Novel Bis‐Thieno[2,3‐b]pyridines and Their Fused Azines

The starting materials pyridine‐2(1H)‐thiones are prepared and reacted with halogen‐containing reagents in ethanolic sodium acetate solution to give the corresponding 2‐S‐alkylpyridines, which cyclized upon their boiling in methanolic sodium methoxide solution at reflux to give the corresponding thieno[2,3‐b]pyridines in excellent yields. Bis (thieno[2,3‐b]pyridine‐2‐carboxamides), incorporating 2,6‐dibromophenoxy moiety, are prepared by the bis‐O‐alkylation of thieno[2,3‐b]pyridine‐2‐carboxamide derivatives. Two synthetic routes are designed to prepare the target molecules pyrido[3′,2′:4,5]thieno[3,2‐d]pyrimidin‐4(3H)‐ones, pyrido[3′,2′:4,5]thieno[3,2‐d][1,2,3]triazin‐4(3H)‐ones, and their bis‐analogues using thieno[2,3‐b]pyridine‐2‐carboxamides and their bis‐analogues. The structure of the target molecules is elucidated using elemental analyses as well as spectral data.     

A Water‐Bridged H‐Bonding Network Contributes to the Catalysis of the SAM‐Dependent C‐Methyltransferase HcgC

[Fe]‐hydrogenase hosts an iron‐guanylylpyridinol (FeGP) cofactor. The FeGP cofactor contains a pyridinol ring substituted with GMP, two methyl groups, and an acylmethyl group. HcgC, an enzyme involved in FeGP biosynthesis, catalyzes methyl transfer from S ‐adenosylmethionine (SAM) to C3 of 6‐carboxymethyl‐5‐methyl‐4‐hydroxy‐2‐pyridinol ( 2 ). We report on the ternary structure of HcgC/S ‐adenosylhomocysteine (SAH, the demethylated product of SAM) and 2 at 1.7 Å resolution. The proximity of C3 of substrate 2 and the S atom of SAH indicates a catalytically productive geometry. The hydroxy and carboxy groups of substrate 2 are hydrogen‐bonded with I115 and T179, as well as through a series of water molecules linked with polar and a few protonatable groups. These interactions stabilize the deprotonated state of the hydroxy groups and a keto form of substrate 2 , through which the nucleophilicity of C3 is increased by resonance effects. Complemented by mutational analysis, a structure‐based catalytic mechanism was proposed.     

Synthetic Study of Carthamin: Biomimetic Synthesis of Carthamin Model via Peroxidase‐Catalyzed Oxidative Decarboxylation of Its Precursor Model

A chiral carthamin model (3S,3′S)‐1‐[5‐acetyl‐2,6‐diketo‐3‐C‐β‐d ‐glucopyranosylcyclohex‐4‐enylidene]‐1′‐[5′‐acetyl‐3′‐C‐β‐d ‐glucopyranosyl‐2′,3′,4′‐trihydroxy‐6′‐oxocyclohexa‐1′,4′‐dienyl]methane, in which two cinnamoyl groups were replaced by an acetyl group, was synthesized by the dimerization of (S)‐2‐acetyl‐4‐C‐(per‐O‐acetyl‐β‐d ‐glucopyranosyl)cyclohexadienone with glyoxylic acid, followed by peroxidase‐catalyzed oxidative decarboxylation and de‐O‐acetylation, or de‐O‐acetylation and peroxidase‐catalyzed oxidative decarboxylation. The corresponding total yields were 12.5% or 17.1% from 3‐C‐(per‐O‐acetyl‐β‐d ‐glucopyranosyl)phloroacetophenone, and the reaction pathway was identical to the biosynthetic pathway.