- Fine-tuning of a radical-based reaction by radical S-adenosyl-L-methionine tryptophan lyase
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The radical S-adenosyl-L-methionine tryptophan lyase NosL converts L-tryptophan into 3-methylindolic acid, which is a precursor in the synthesis of the thiopeptide antibiotic nosiheptide. Using electron paramagnetic resonance spectroscopy and multiple L-tryptophan isotopologues, we trapped and characterized radical intermediates that indicate a carboxyl fragment migration mechanism for NosL. This is in contrast to a proposed fragmentation-recombination mechanism that implied Cα-Cβ bond cleavage of L-tryptophan. Although NosL resembles related tyrosine lyases, subtle substrate motions in its active site are responsible for a fine-tuned radical chemistry, which selects the Cα-C bond for disruption. This mechanism highlights evolutionary adaptation to structural constraints in proteins as a route to alternative enzyme function.
- Sicoli, Giuseppe,Mouesca, Jean-Marie,Zeppieri, Laura,Amara, Patricia,Martin, Lydie,Barra, Anne-Laure,Fontecilla-Camps, Juan C.,Gambarelli, Serge,Nicolet, Yvain
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- Mechanistic study of the radical SAM-dependent amine dehydrogenation reactions
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The radical SAM enzyme NosL catalyzes the conversion of l-Trp to 3-methyl-2-indolic acid, and this reaction is initiated by the 5′-deoxyadenosyl (dAdo) radical-mediated hydrogen abstraction from the l-Trp amino group. We demonstrate here that when d-Trp was used in the NosL reaction, hydrogen abstraction occurs promiscuously at both the amino group and Cα of d-Trp. These results inspired us to establish the detailed mechanism of l-Trp amine dehydrogenation catalyzed by a NosL mutant, and to engineer a novel radical SAM-dependent l-Tyr amine dehydrogenase from the thiamine biosynthesis enzyme ThiH.
- Ji, Xinjian,Liu, Wan-Qiu,Yuan, Shuguang,Yin, Yue,Ding, Wei,Zhang, Qi
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- Synthesis of the core structure of phalarine
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The core skeleton of phalarine was rapidly synthesised through novel palladium-catalysed dearomative spirocyclisation and a palladium-catalysed Wacker-carbonylative cyclisation cascade. The two key steps allowed for the efficient construction of a tricyclic propeller skeleton bearing contiguous tetrasubstituted carbon centres, within 3 steps from a topologically planar precursor.
- Douki, Kazuya,Shimokawa, Jun,Kitamura, Masato
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- Radical-mediated enzymatic carbon chain fragmentation-recombination
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The radical S-adenosylmethionine (S-AdoMet) superfamily contains thousands of proteins that catalyze highly diverse conversions, most of which are poorly understood, owing to a lack of information regarding chemical products and radical-dependent transformations. We here report that NosL, involved in forming the indole side ring of the thiopeptide nosiheptide (NOS), is a radical S-AdoMet 3-methyl-2-indolic acid (MIA) synthase. NosL catalyzed an unprecedented carbon chain reconstitution of L-tryptophan to give MIA, showing removal of the C' ±-N unit and shift of the carboxylate to the indole ring. Dissection of the enzymatic process upon the identification of products and a putative glycyl intermediate uncovered a radical-mediated, unusual fragmentation- recombination reaction. This finding unveiled a key step in radical S-AdoMet enzyme-catalyzed structural rearrangements during complex biotransformations. Additionally, NosL tolerated fluorinated L-tryptophan as the substrate, allowing for production of a regiospecifically halogenated thiopeptide that has not been found among the more than 80 members of the naturally occurring thiopeptide family.
- Zhang, Qi,Li, Yuxue,Chen, Dandan,Yu, Yi,Duan, Lian,Shen, Ben,Liu, Wen
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- Tryptophan Lyase (NosL): A Cornucopia of 5′-Deoxyadenosyl Radical Mediated Transformations
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Tryptophan lyase (NosL) is a radical S-adenosyl-l-methionine (SAM) enzyme that catalyzes the formation of 3-methyl-2-indolic acid from l-tryptophan. In this paper, we demonstrate that the 5′-deoxyadenosyl radical is considerably more versatile in its chem
- Bhandari, Dhananjay M.,Fedoseyenko, Dmytro,Begley, Tadhg P.
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- Mechanistic Studies on Tryptophan Lyase (NosL): Identification of Cyanide as a Reaction Product
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Tryptophan lyase (NosL) catalyzes the formation of 3-methylindole-2-carboxylic acid and 3-methylindole from l-tryptophan. In this paper, we provide evidence supporting a formate radical intermediate and demonstrate that cyanide is a byproduct of the NosL-catalyzed reaction with l-tryptophan. These experiments require a major revision of the NosL mechanism and uncover an unanticipated connection between NosL and HydG, the radical SAM enzyme that forms cyanide and carbon monoxide from tyrosine during the biosynthesis of the metallo-cluster of the [Fe-Fe] hydrogenase.
- Bhandari, Dhananjay M.,Fedoseyenko, Dmytro,Begley, Tadhg P.
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- Crystal structure of tryptophan lyase (NosL): Evidence for radical formation at the amino group of tryptophan
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Streptomyces actuosus tryptophan lyase (NosL) is a radical SAM enzyme which catalyzes the synthesis of 3-methyl-2-indolic acid, a precursor in the synthesis of the promising antibiotic nosiheptide. The reaction involves cleavage of the tryptophan Cα-Cβ bond and recombination of the amino-acid-derived-COOH fragment at the indole ring. Reported herein is the 1.8 ? resolution crystal structure of NosL complexed with its substrate. Unexpectedly, only one of the tryptophan amino hydrogen atoms is optimally placed for H abstraction by the SAM-derived 5'-deoxyadenosyl radical. This orientation, in turn, rules out the previously proposed delocalized indole radical as the species which undergoes Cα-Cβ bond cleavage. Instead, stereochemical considerations indicate that the reactive intermediate is a ·NH tryptophanyl radical. A structure-based amino acid sequence comparison of NosL with the tyrosine lyases ThiH and HydG strongly suggests that an equivalent ·NH radical operates in the latter enzymes.
- Nicolet, Yvain,Zeppieri, Laura,Amara, Patricia,Fontecilla-Camps, Juan C.
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- Mechanistic Insights into the Radical S-adenosyl- l -methionine Enzyme NosL from a Substrate Analogue and the Shunt Products
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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 i
- Ji, Xinjian,Li, Yongzhen,Jia, Youli,Ding, Wei,Zhang, Qi
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- Substrate-Tuned Catalysis of the Radical S-Adenosyl- L -Methionine Enzyme NosL Involved in Nosiheptide Biosynthesis
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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.
- Ji, Xinjian,Li, Yongzhen,Ding, Wei,Zhang, Qi
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- POSITIVE ALLOSTERIC MODULATORS OF THE GLP-1 RECEPTOR
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Described are positive allosteric modulators of the GLP-1 receptor, pharmaceutical compositions including the compounds, and methods of using the compounds and compositions for diabetes mellitus type 2, obesity, depression, Alzheimer's disease, Parkinson's disease, Huntington's disease, stroke, cognitive dysfunction, learning disability, and asthma in a subject.
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Paragraph 00251
(2017/07/31)
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- The Catalytic Mechanism of the Class C Radical S-Adenosylmethionine Methyltransferase NosN
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S-Adenosylmethionine (SAM) is one of the most common co-substrates in enzyme-catalyzed methylation reactions. Most SAM-dependent reactions proceed through an SN2 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.
- Ding, Wei,Li, Yongzhen,Zhao, Junfeng,Ji, Xinjian,Mo, Tianlu,Qianzhu, Haocheng,Tu, Tao,Deng, Zixin,Yu, Yi,Chen, Fener,Zhang, Qi
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supporting information
p. 3857 - 3861
(2017/03/27)
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- Expanding Radical SAM Chemistry by Using Radical Addition Reactions and SAM Analogues
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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.
- Ji, Xinjian,Li, Yongzhen,Xie, Liqi,Lu, Haojie,Ding, Wei,Zhang, Qi
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p. 11845 - 11848
(2016/11/16)
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- Rearrangement of 3,3-disubstituted indolenines and synthesis of 2,3-substituted indoles
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(Diagram presented) Synthesis of 2,3-substituted indoles from phenylhydrazine and α-branched aldehydes via rearrangement of 3,3-disubstituted indolenine intermediates is reported.
- Liu, Kevin G.,Robichaud, Albert J.,Lo, Jennifer R.,Mattes, James F.,Cai, Yanxuan
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p. 5769 - 5771
(2007/10/03)
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- Probing the subpockets of factor Xa reveals two binding modes for inhibitors based on a 2-carboxyindole scaffold: A study combining structure-activity relationship and X-ray crystallography
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Structure-activity relationships within a series of highly potent 2-carboxyindole-based factor Xa inhibitors incorporating a neutral P1 ligand are described with particular emphasis on the structural requirements for addressing subpockets of the factor Xa enzyme. Interactions with the subpockets were probed by systematic substitution of the 2-carboxyindole scaffold, in combination with privileged P1 and P4 substituents. Combining the most favorable substituents at the indole nucleus led to the discovery of a remarkably potent factor Xa inhibitor displaying a Ki value of 0.07 nM. X-ray crystallography of inhibitors bound to factor Xa revealed substituent-dependent switching of the inhibitor binding mode and provided a rationale for the SAR obtained. These results underscore the key role played by the P1 ligand not only in determining the binding affinity of the inhibitor by direct interaction but also in modifying the binding mode of the whole scaffold, resulting in a nonlinear SAR.
- Nazaré, Marc,Will, David W.,Matter, Hans,Schreuder, Herman,Ritter, Kurt,Urmann, Matthias,Essrich, Melanie,Bauer, Armin,Wagner, Michael,Czech, J?rg,Lorenz, Martin,Laux, Volker,Wehner, Volkmar
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p. 4511 - 4525
(2007/10/03)
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- Analogs of indole-3-carbinol metabolites as chemotherapeutic and chemopreventive agents
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Novel compounds useful as chemotherapeutic and chemopreventive agents are provided. The compounds are analogs of indole-3-carbinol metabolites wherein the structures and substituents of the compounds are selected to enhance the compounds' overall efficacy, particularly with respect to therapeutic activity, oral bioavailability, long-term safety, patient tolerability, and therapeutic window. The compounds are useful not only in treatment of cancer but also in prevention of cancer. One preferred class of the novel compounds have the structure of formula (I) wherein R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11, and R12 are defined herein. Pharmaceutical compositions are provided as well, as are methods of synthesis and use.
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Page/Page column 21-22
(2008/06/13)
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- Anti-aids piperazines
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The present invention includes diaromatic substituted heterocyclic compounds (III) STR1 which are useful in treating individuals infected with the HIV virus. The invention includes certain previously generically disclosed anti-AIDS piperazinyl compounds (V) and a method of treating HIV infected individuals with the indoles of formula (V) and the anti-AIDS amines (X).
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