Mechanistic Insights into the Radical S‐adenosyl‐l‐methionine Enzyme NosL From a Substrate Analogue and the Shunt Products

The radical S‐adenosyl‐l ‐methionine (SAM) enzyme NosL catalyzes the transformation of l ‐tryptophan into 3‐methyl‐2‐indolic acid (MIA), which is a key intermediate in the biosynthesis of a clinically interesting antibiotic nosiheptide. NosL catalysis was investigated by using the substrate analogue 2‐methyl‐3‐(indol‐3‐yl)propanoic acid (MIPA), which can be converted into MIA by NosL. Biochemical assays with different MIPA isotopomers in D₂O and H₂O unambiguously indicated that the 5′‐deoxyadenosyl (dAdo)‐radical‐mediated hydrogen abstraction is from the amino group of l ‐tryptophan and not a protein residue. Surprisingly, the dAdo‐radical‐mediated hydrogen abstraction occurs at two different sites of MIPA, thereby partitioning the substrate into different reaction pathways. Together with identification of an α,β‐unsaturated ketone shunt product, our study provides valuable mechanistic insight into NosL catalysis and highlights the remarkable catalytic flexibility of radical SAM enzymes.     

Substrate‐Tuned Catalysis of the Radical S‐Adenosyl‐L‐Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis

NosL is a radical S‐adenosyl‐L ‐methionine (SAM) enzyme that converts L ‐Trp to 3‐methyl‐2‐indolic acid, a key intermediate in the biosynthesis of a thiopeptide antibiotic nosiheptide. In this work we investigated NosL catalysis by using a series of Trp analogues as the molecular probes. Using a benzofuran substrate 2‐amino‐3‐(benzofuran‐3‐yl)propanoic acid (ABPA), we clearly demonstrated that the 5′‐deoxyadenosyl (dAdo) radical‐mediated hydrogen abstraction in NosL catalysis is not from the indole nitrogen but likely from the amino group of L ‐Trp. Unexpectedly, the major product of ABPA is a decarboxylated compound, indicating that NosL was transformed to a novel decarboxylase by an unnatural substrate. Furthermore, we showed that, for the first time to our knowledge, the dAdo radical‐mediated hydrogen abstraction can occur from an alcohol hydroxy group. Our study demonstrates the intriguing promiscuity of NosL catalysis and highlights the potential of engineering radical SAM enzymes for novel activities.     

Radical Stability Directs Electron Capture and Transfer Dissociation of β‐Amino Acids in Peptides

We report on the characteristics of the radical‐ion‐driven dissociation of a diverse array of β‐amino acids incorporated into α‐peptides, as probed by tandem electron‐capture and electron‐transfer dissociation (ECD/ETD) mass spectrometry. The reported results demonstrate a stronger ECD/ETD dependence on the nature of the amino acid side chain for β‐amino acids than for their α‐form counterparts. In particular, only aromatic (e.g., β‐Phe), and to a substantially lower extent, carbonyl‐containing (e.g., β‐Glu and β‐Gln) amino acid side chains, lead to N? C_β bond cleavage in the corresponding β‐amino acids. We conclude that radical stabilization must be provided by the side chain to enable the radical‐driven fragmentation from the nearby backbone carbonyl carbon to proceed. In contrast with the cleavage of backbones derived from α‐amino acids, ECD of peptides composed mainly of β‐amino acids reveals a shift in cleavage priority from the N? C_β to the C_α? C bond. The incorporation of CH₂ groups into the peptide backbone may thus drastically influence the backbone charge solvation preference. The characteristics of radical‐driven β‐amino acid dissociation described herein are of particular importance to methods development, applications in peptide sequencing, and peptide and protein modification (e.g., deamidation and isomerization) analysis in life science research.     

Estimation of peptide N–Cα bond cleavage efficiency during MALDI‐ISD using a cyclic peptide

Matrix‐assisted laser desorption/ionization in‐source decay (MALDI‐ISD) induces N–C_α bond cleavage via hydrogen transfer from the matrix to the peptide backbone, which produces a c′/z? fragment pair. Subsequently, the z? generates z′ and [z + matrix] fragments via further radical reactions because of the low stability of the z?. In the present study, we investigated MALDI‐ISD of a cyclic peptide. The N–C_α bond cleavage in the cyclic peptide by MALDI‐ISD produced the hydrogen‐abundant peptide radical [M + 2H]⁺? with a radical site on the α‐carbon atom, which then reacted with the matrix to give [M + 3H]⁺ and [M + H + matrix]⁺. For 1,5‐diaminonaphthalene (1,5‐DAN) adducts with z fragments, post‐source decay of [M + H + 1,5‐DAN]⁺ generated from the cyclic peptide showed predominant loss of an amino acid with 1,5‐DAN. Additionally, MALDI‐ISD with Fourier transform‐ion cyclotron resonance mass spectrometry allowed for the detection of both [M + 3H]⁺ and [M + H]⁺ with two ¹³C atoms. These results strongly suggested that [M + 3H]⁺ and [M + H + 1,5‐DAN]⁺ were formed by N–C_α bond cleavage with further radical reactions. As a consequence, the cleavage efficiency of the N–C_α bond during MALDI‐ISD could be estimated by the ratio of the intensity of [M + H]⁺ and [M + 3H]⁺ in the Fourier transform‐ion cyclotron resonance spectrum. Because the reduction efficiency of a matrix for the cyclic peptide cyclo(Arg‐Gly‐Asp‐D‐Phe‐Val) was correlated to its tendency to cleave the N–C_α bond in linear peptides, the present method could allow the evaluation of the efficiency of N–C_α bond cleavage for MALDI matrix development. Copyright © 2016 John Wiley & Sons, Ltd.     

Ion‐Induced Fragmentation of Amino Acids: Effect of the Environment

In general, radiation‐induced fragmentation of small amino acids is governed by the cleavage of the C? C_α bond. We present results obtained with 300 keV Xe²⁰⁺ ions that allow molecules (glycine and valine) to be ionised at large distances without appreciable energy transfer. Also in the present case, the C? C_α bond turns out to be the weakest link and hence its scission is the dominant fragmentation channel. Intact ionised molecules are observed with very low intensities. When the molecules are embedded in a cluster of amino acids, a protective effect of the environment is observed. The fragmentation pattern changes: the C? C_α bond becomes more protected and stable amino acid cations are observed as fragments of the molecular clusters. Evidently, the molecular cluster acts as a “buffer” for the excess energy, capable of rapidly redistributing excess energy and charge.     

New Tryptophan Metabolites from Cultures of the Lipophilic Yeast Malassezia furfur

Eleven new indole alkaloids were isolated from cultures of the human pathogenic yeast Malassezia furfur after addition of L ‐tryptophan as the sole N‐source: pityriacitrin B ( 2 ), the malassezindoles A ( 3 ) and B ( 4 ), malassezialactic acid ( 6 ), the malasseziazoles A ( 7 ), B ( 8 ), and C ( 9 ), pityriazole ( 10 ), malasseziacitrin ( 11 ), and malassezione ( 12 ), along with the known d‐ indole‐3‐lactic acid (=(αR)‐α‐hydroxy‐1H‐indole‐3‐propanoic acid 5 ), and 2‐hydroxy‐1‐(1H‐indol‐3‐yl)ethanone ( 13 ). The structural elucidation of these compounds was performed by spectroscopic methods (MS as well as 1D‐ and 2D‐NMR). The biogenetic relationships (Scheme) and biological activities of the new metabolites are discussed.     

Catalytic Carbocation Generation Enabled by the Mesolytic Cleavage of Alkoxyamine Radical Cations

A new catalytic method is described to access carbocation intermediates via the mesolytic cleavage of alkoxyamine radical cations. In this process, electron transfer between an excited state oxidant and a TEMPO‐derived alkoxyamine substrate gives rise to a radical cation with a remarkably weak C?O bond. Spontaneous scission results in the formation of the stable nitroxyl radical TEMPO^. as well as a reactive carbocation intermediate that can be intercepted by a wide range of nucleophiles. Notably, this process occurs under neutral conditions and at comparatively mild potentials, enabling catalytic cation generation in the presence of both acid sensitive and easily oxidized nucleophilic partners.     

Total Synthesis of cis‐Clavicipitic Acid from Asparagine via Ir‐Catalyzed CH bond Activation as a Key Step

4‐Substituted tryptophan derivatives and the total synthesis of cis‐clavicipitic acid were achieved in reactions in which Ir‐catalyzed C?H bond activation was a key step. The starting material for these reactions is asparagine, which is a cheap natural amino acid. The reductive amination step from the 4‐substituted tryptophan derivative gave cis‐clavicipitic acid with perfect diastereoselectivity.     

Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues

Radical S‐adenosyl‐l ‐methionine (SAM) enzymes utilize a [4Fe‐4S] cluster to bind SAM and reductively cleave its carbon–sulfur bond to produce a highly reactive 5′‐deoxyadenosyl (dAdo) radical. In almost all cases, the dAdo radical abstracts a hydrogen atom from the substrates or from enzymes, thereby initiating a highly diverse array of reactions. Herein, we report a change of the dAdo radical‐based chemistry from hydrogen abstraction to radical addition in the reaction of the radical SAM enzyme NosL. This change was achieved by using a substrate analogue containing an olefin moiety. We also showed that two SAM analogues containing different nucleoside functionalities initiate the radical‐based reactions with high efficiencies. The radical adduct with the olefin produced in the reaction was found to undergo two divergent reactions, and the mechanistic insights into this process were investigated in detail. Our study demonstrates a promising strategy in expanding radical SAM chemistry, providing an effective way to access nucleoside‐containing compounds by using radical SAM‐dependent reactions.     

Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry

The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSⁿ tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at C_β by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at C_α is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd.     

Monofluoroalkenylation of Dimethylamino Compounds through Radical–Radical Cross‐Coupling

An unprecedented and challenging radical–radical cross‐coupling of α‐aminoalkyl radicals with monofluoroalkenyl radicals derived from gem‐difluoroalkenes was achieved. This first example of tandem C(sp³)?H and C(sp²)?F bond functionalization through visible‐light photoredox catalysis offers a facile and flexible access to privileged tetrasubstituted monofluoroalkenes under very mild reaction conditions. The striking features of this redox‐neutral method in terms of scope, functional‐group tolerance, and regioselectivity are illustrated by the late‐stage fluoroalkenylation of complex molecular architectures such as bioactive (+)‐diltiazem, rosiglitazone, dihydroartemisinin, oleanic acid, and androsterone derivatives, which represent important new α‐amino C?H monofluoroalkenylations.     

Density Functional Studies on Thromboxane Biosynthesis: Mechanism and Role of the Heme‐Thiolate System

Reaction mechanisms for the isomerization of prostaglandin H₂ to thromboxane A₂, and degradation to 12‐L‐hydroxy‐5,8,10‐heptadecatrienoic acid (HHT) and malondialdehyde (MDA), catalyzed by thromboxane synthase, were investigated using the unrestricted Becke‐three‐parameter plus Lee–Yang–Parr (UB3LYP) density functional level theory. In addition to the reaction pathway through Fe^IV‐porphyrin intermediates, a new reaction pathway through Fe^III‐porphyrin π‐cation radical intermediates was found. Both reactions proceed with the homolytic cleavage of endoperoxide O? O to give an alkoxy radical. This intermediate converts into an allyl radical intermediate by a C? C homolytic cleavage, followed by the formation of thromboxane A₂ having a 6‐membered ring through a one electron transfer, or the degradation into HHT and MDA. The proposed mechanism shows that an iron(III)‐containing system having electron acceptor ability is essential for the 6‐membered ring formation leading to thromboxane A₂. Our results suggest that the step of the endoperoxide O? O homolytic bond cleavage has the highest activation energy following the binding of prostaglandin H₂ to thromboxane synthase.     

Palladium/Norbornene‐Catalyzed C−H Alkylation/Alkyne Insertion/Indole Dearomatization Domino Reaction: Assembly of Spiroindolenine‐Containing Pentacyclic Frameworks

Reported is a highly chemoselective intermolecular annulation of indole‐based biaryls with bromoalkyl alkynes by using palladium/norbornene (Pd/NBE) cooperative catalysis. This reaction is realized through a sequence of Catellani‐type C?H alkylation, alkyne insertion, and indole dearomatization, by forming two C(sp²)?C(sp³) and one C(sp²)?C(sp²) bonds in a single chemical operation, thus providing a diverse range of pentacyclic molecules, containing a spiroindolenine fragment, in good yields with excellent functional‐group tolerance. Preliminary mechanistic studies reveal that C?H bond cleavage is likely involved in the rate‐determining step, and the indole dearomatization might take place through an olefin coordination/insertion and β‐hydride elimination Heck‐type pathway.     

Ruthenium(II)‐Catalyzed Traceless C−H Functionalization Using an N−N Bond as an Internal Oxidant

A previously elusive Ru^II‐catalyzed N?N bond‐based traceless C?H functionalization strategy is reported. An N‐amino (i.e., hydrazine) group is used for the directed C?H functionalization with either an alkyne or an alkene, affording an indole derivative or olefination product. The synthesis features a broad substrate scope, superior atom and step economy, as well as mild reaction conditions.     

Amino Acid Derived Phosphine‐Catalyzed Enantioselective 1,4‐Dipolar Spiroannulation of Cyclobutenones and Isatylidenemalononitrile

Cyclobutenones have been explored as a new type of chiral 1,4‐dipole four‐carbon synthon, which readily undergoes organophosphine‐mediated C?C bond cleavage and asymmetric intermolecular 1,4‐dipolar spiroannulation with isatylidenemalononitrile in the presence of amino acid‐derived chiral phosphine catalyst to furnish enantioenriched 3‐spirocyclohexenone 2‐oxindoles in good yield with up to 87 % ee. To our knowledge, this is the first example of asymmetric transformation of cyclobutenones and the phosphine‐catalyzed asymmetric 1,4‐dipolar cycloaddition consisting of C?C bond activation is unprecedented.     

Dye‐Labeled Cα‐Tetrasubstituted α‐Amino Acids

We report the synthesis of pyrene‐ and carboxyfluorescein labeled C^α‐tetrasubstituted amino acids (TAAs). The fluorescent dye can be coupled to the TAA before or after its incorporation into a peptide sequence using a Suzuki‐type C? C bond formation.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

Through‐Space 1,4‐Palladium Migration and 1,2‐Aryl Shift: Direct Access to Dibenzo[a,c]carbazoles through a Triple CH Functionalization Cascade

A palladium‐catalyzed expeditious synthesis of dibenzofused carbazoles from readily available 2‐arylindoles and diaryliodonium salts is reported. Interestingly, after the electrophilic C3 palladation of indole, an unexpected “through‐space” 1,4‐palladium migration to the 2‐aryl moiety, by remote C?H bond activation followed by C?H arylation with diaryliodonium salt, and an unprecedented 1,2‐aryl shift take place. Finally, an intramolecular cross‐dehydrogenative coupling (CDC) at the C2 position affords dibenzo[a,c]carbazoles in high yields. Remarkably, the present migratory annulation occurs through three C?H bond activation one C?C bond cleavage, and the simultaneous construction of three new C?C bonds in a single operation.     

Rhodium(III)‐Catalyzed CH Activation and Indole Synthesis With Hydrazone as an Auto‐Formed and Auto‐Cleavable Directing Group

An efficient, practical, and external‐oxidant‐free indole synthesis from readily available aryl hydrazines was developed, by using hydrazone as a directing group for Rh^III‐catalyzed C?H activation and alkyne annulation. The hydrazone group was formed by in situ condensation of hydrazines and C?O source, whereas its N?N bond was served as an internal oxidant, for which we termed it as an auto‐formed and auto‐cleavable directing group (DG^auto). This method needs no step for pre‐installation and post‐cleavage of the directing group, making it a quite easily scalable approach to access unprotected indoles with high step economy. The DG^auto strategy was also applicable for isoquinoline synthesis. In addition, synthetic utilities of this chemistry for rapid assembly of π‐extended nitrogen‐doped polyheterocycles and bioactive molecules were demonstrated.     

Hypervalent radical formation probed by electron transfer dissociation of zwitterionic tryptophan and tryptophan‐containing dipeptides complexed with Ca2+ and 18‐crown‐6 in the gas phase

The relationship between peptide structure and electron transfer dissociation (ETD) is important for structural analysis by mass spectrometry. In the present study, the formation, structure and reactivity of the reaction intermediate in the ETD process were examined using a quadrupole ion trap mass spectrometer equipped with an electrospray ionization source. ETD product ions of zwitterionic tryptophan (Trp) and Trp‐containing dipeptides (Trp‐Gly and Gly‐Trp) were detected without reionization using non‐covalent analyte complexes with Ca²⁺ and 18‐crown‐6 (18C6). In the collision‐induced dissociation, NH₃ loss was the main dissociation pathway, and loss related to the dissociation of the carboxyl group was not observed. This indicated that Trp and its dipeptides on Ca²⁺(18C6) adopted a zwitterionic structure with an NH₃⁺ group and bonded to Ca²⁺(18C6) through the COO^? group. Hydrogen atom loss observed in the ETD spectra indicated that intermolecular electron transfer from a molecular anion to the NH₃⁺ group formed a hypervalent ammonium radical, R‐NH₃, as a reaction intermediate, which was unstable and dissociated rapidly through N–H bond cleavage. In addition, N–C_α bond cleavage forming the z₁ ion was observed in the ETD spectra of Trp‐GlyCa²⁺(18C6) and Gly‐TrpCa²⁺(18C6). This dissociation was induced by transfer of a hydrogen atom in the cluster formed via an N–H bond cleavage of the hypervalent ammonium radical and was in competition with the hydrogen atom loss. The results showed that a hypervalent radical intermediate, forming a delocalized hydrogen atom, contributes to the backbone cleavages of peptides in ETD. Copyright © 2015 John Wiley & Sons, Ltd.