scholarly journals Structural Basis for an Unprecedented Enzymatic Alkylation in Cylindrocyclophane Biosynthesis

2021 ◽  
Author(s):  
Nathaniel R. Braffman ◽  
Terry B. Ruskoski ◽  
Katherine M. Davis ◽  
Nate Glasser ◽  
Cassidy Johnson ◽  
...  
Keyword(s):  
Alkyl Halide ◽  
Bioinformatic Analysis ◽  
Enzyme Engineering ◽  
Catalyst Design ◽  
Alkyl Halides ◽  
Structural Basis ◽  
Aromatic Rings ◽  
Carbon Carbon Bonds ◽  
Dynamics Simulations ◽  
Alkylation Reactions

AbstractThe cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon-carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology and the structure and mechanism of CylK are unknown. Here, we report x-ray crystal structures of CylK, revealing a distinctive fusion of a Ca2+ binding domain and a β-propeller fold. We use a mutagenic screening approach to locate CylK’s active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicates Asp440 and Glu374 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.

scholarly journals Direct C(sp2)–H alkylation of unactivated arenes enabled by photoinduced Pd catalysis

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Daeun Kim ◽  
Geun Seok Lee ◽  
Dongwook Kim ◽  
Soon Hyeok Hong
Keyword(s):  
Functional Group ◽  
Alkyl Halide ◽  
Alkyl Halides ◽  
Biologically Active ◽  
One Pot ◽  
Bond Forming ◽  
Alkyl Groups ◽  
Alkyl Bromides ◽  
Reaction Proceeds ◽  
Alkylation Reactions

AbstractDespite the fundamental importance of efficient and selective synthesis of widely useful alkylarenes, the direct catalytic C(sp2)–H alkylation of unactivated arenes with a readily available alkyl halide remains elusive. Here, we report the catalytic C(sp2)–H alkylation reactions of unactivated arenes with alkyl bromides via visible-light induced Pd catalysis. The reaction proceeds smoothly under mild conditions without any skeletal rearrangement of the alkyl groups. The direct syntheses of structurally diverse linear and branched alkylarenes, including the late-stage phenylation of biologically active molecules and an orthogonal one-pot sequential Pd-catalyzed C–C bond-forming reaction, are achieved with exclusive chemoselectivity and exceptional functional group tolerance. Comprehensive mechanistic investigations through a combination of experimental and computational methods reveal a distinguishable Pd(0)/Pd(I) redox catalytic cycle and the origin of the counter-intuitive reactivity differences among alkyl halides.

scholarly journals Structure and assembly of the diiron cofactor in the heme-oxygenase–like domain of the N-nitrosourea–producing enzyme SznF

2021 ◽  
Vol 118 (4) ◽  
pp. e2015931118
Author(s):  
Molly J. McBride ◽  
Sarah R. Pope ◽  
Kai Hu ◽  
C. Denise Okafor ◽  
Emily P. Balskus ◽  
...  
Keyword(s):  
Heme Oxygenase ◽  
Large Scale ◽  
Recent Observation ◽  
Nonheme Iron ◽  
The Other ◽  
Structural Basis ◽  
Carboxylate Ligand ◽  
Cancer Drug ◽  
Carbon Carbon Bonds ◽  
Dynamics Simulations

In biosynthesis of the pancreatic cancer drug streptozotocin, the tridomain nonheme-iron oxygenase SznF hydroxylates Nδ and Nω′ of Nω-methyl-l-arginine before oxidatively rearranging the triply modified guanidine to the N-methyl-N-nitrosourea pharmacophore. A previously published structure visualized the monoiron cofactor in the enzyme’s C-terminal cupin domain, which promotes the final rearrangement, but exhibited disorder and minimal metal occupancy in the site of the proposed diiron cofactor in the N-hydroxylating heme-oxygenase–like (HO-like) central domain. We leveraged our recent observation that the N-oxygenating µ-peroxodiiron(III/III) intermediate can form in the HO-like domain after the apo protein self-assembles its diiron(II/II) cofactor to solve structures of SznF with both of its iron cofactors bound. These structures of a biochemically validated member of the emerging heme-oxygenase–like diiron oxidase and oxygenase (HDO) superfamily with intact diiron cofactor reveal both the large-scale conformational change required to assemble the O2-reactive Fe2(II/II) complex and the structural basis for cofactor instability—a trait shared by the other validated HDOs. During cofactor (dis)assembly, a ligand-harboring core helix dynamically (un)folds. The diiron cofactor also coordinates an unanticipated Glu ligand contributed by an auxiliary helix implicated in substrate binding by docking and molecular dynamics simulations. The additional carboxylate ligand is conserved in another N-oxygenating HDO but not in two HDOs that cleave carbon–hydrogen and carbon–carbon bonds to install olefins. Among ∼9,600 sequences identified bioinformatically as members of the emerging HDO superfamily, ∼25% conserve this additional carboxylate residue and are thus tentatively assigned as N-oxygenases.

scholarly journals Structural Basis for the Friedel-Crafts Alkylation in Cylindrocyclophane Biosynthesis

2021 ◽  
Author(s):  
Hua-Qi Wang ◽  
Shu-Bin Mou ◽  
Wen Xiao ◽  
Huan Zhou ◽  
Xu-Dong Hou ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Organic Synthesis ◽  
Catalytic Mechanism ◽  
Alkyl Halide ◽  
Activation Mechanism ◽  
Structural Basis ◽  
Key Enzyme ◽  
Double Activation ◽  
Energy Simulations ◽  
Alkylation Reactions

The Lewis acid-catalyzed Friedel-Crafts alkylation of an aromatic ring with an alkyl halide is extensively used in organic synthesis. However, its biological counterpart was not reported until the elucidation of the cylindrocyclophane biosynthetic pathway in Cylindrospermum licheniforme ATCC 29412 by Balskus and co-workers. CylK is the key enzyme to catalyze the formation of the cylindrocyclophane scaffold through the Friedel-Crafts alkylation reactions with regioselectivity and stereospecificity. Further research demonstrates that CylK can accept other resorcinol rings and secondary alkyl halides as substrates. To date, the crystal structure of CylK has not been disclosed and the catalytic mechanism remains obscure. Herein we report the crystal structures of CylK in its apo form and its complexes with the analogues of its substrate and reaction intermediate. Combining the crystal structures, free energy simulations and the mutagenesis experiments, we proposed a concerted double-activation mechanism, which could explain the regioselectivity and stereospecificity. This work provides a foundation for engineering CylK as a biocatalyst to expand its substrate scope and applications in organic synthesis.

Transition state analysis. I. Correlation between solvent stretching frequencies and C vs. O product ratios in alkylation of ambient anions. A new explanation for the observed product ratios

1970 ◽  
Vol 48 (13) ◽  
pp. 2120-2123 ◽  
Author(s):  
Donald C. Wigfield
Keyword(s):  
Free Energy ◽  
Phenolic Compounds ◽  
Ground State ◽  
Metal Cation ◽  
Alkyl Halide ◽  
Alkyl Halides ◽  
Linear Free Energy Relationships ◽  
Linear Free Energy ◽  
Energy Relationships ◽  
Alkylation Reactions

A new explanation is presented for the O to C product ratios observed in alkylation reactions of ethyl acetoacetate and related enolic and phenolic compounds, based on a Hammond postulate analysis of the nature of the transition states involved. The explanation not only covers the effects of solvent and the nature of the metal cation, but also encompasses the previously unexplained effect of the alkyl halide structure. From the latter effect, ground state interaction between solvent and alkyl halide is predicted. Evidence consistent with this interaction is found in linear free energy relationships between the ΔΔG‡ (C vs. O) values for various alkyl halides and the stretching frequency of the solvent (S=O of DMSO; P=O of HMPA) when measured as alkyl halide solutions.

scholarly journals Cobalt-catalyzed directed alkylation of arenes with primary and secondary alkyl halides

2014 ◽  
Vol 86 (3) ◽  
pp. 419-424 ◽  
Author(s):  
Naohiko Yoshikai ◽  
Ke Gao
Keyword(s):  
Alkyl Radical ◽  
Room Temperature ◽  
Alkylating Agents ◽  
Alkyl Halide ◽  
Alkyl Halides ◽  
Single Electron Transfer ◽  
Directing Group ◽  
Aromatic Imines ◽  
Alkylation Reactions ◽  
Cobalt Species

Abstract A cobalt–N-heterocyclic carbene catalyst allows ortho-alkylation of aromatic imines with unactivated primary and secondary alkyl chlorides and bromides under room-temperature conditions. The scope of the reaction encompasses or complements that of cobalt-catalyzed ortho-alkylation reactions with olefins as alkylating agents that we developed previously. Stereochemical outcomes of secondary alkylation reactions suggest that the reaction involves single-electron transfer from a cobalt species to the alkyl halide to generate the corresponding alkyl radical. A cycloalkylated product obtained by this method can be transformed into unique spirocycles through manipulation of the directing group and the cycloalkyl groups.

scholarly journals Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bertrand Beckert ◽  
Elodie C. Leroy ◽  
Shanmugapriya Sothiselvam ◽  
Lars V. Bock ◽  
Maxim S. Svetlov ◽  
...  
Keyword(s):  
Antibiotic Resistance Genes ◽  
Structural Basis ◽  
Sequence Motifs ◽  
Specific Sequence ◽  
Bacterial Ribosome ◽  
Translational Arrest ◽  
Exit Tunnel ◽  
Mechanistic Basis ◽  
Dynamics Simulations ◽  
Context Specific

AbstractMacrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.

Discovery of natural product ovalicin sensitive type 1 methionine aminopeptidases: molecular and structural basis

2019 ◽  
Vol 476 (6) ◽  
pp. 991-1003 ◽  
Author(s):  
Vijaykumar Pillalamarri ◽  
Tarun Arya ◽  
Neshatul Haque ◽  
Sandeep Chowdary Bala ◽  
Anil Kumar Marapaka ◽  
...  
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Covalent Modification ◽  
Structural Basis ◽  
Wild Type ◽  
Methionine Aminopeptidases ◽  
Synthetic Derivative ◽  
Dynamics Simulations

Abstract Natural product ovalicin and its synthetic derivative TNP-470 have been extensively studied for their antiangiogenic property, and the later reached phase 3 clinical trials. They covalently modify the conserved histidine in Type 2 methionine aminopeptidases (MetAPs) at nanomolar concentrations. Even though a similar mechanism is possible in Type 1 human MetAP, it is inhibited only at millimolar concentration. In this study, we have discovered two Type 1 wild-type MetAPs (Streptococcus pneumoniae and Enterococcus faecalis) that are inhibited at low micromolar to nanomolar concentrations and established the molecular mechanism. F309 in the active site of Type 1 human MetAP (HsMetAP1b) seems to be the key to the resistance, while newly identified ovalicin sensitive Type 1 MetAPs have a methionine or isoleucine at this position. Type 2 human MetAP (HsMetAP2) also has isoleucine (I338) in the analogous position. Ovalicin inhibited F309M and F309I mutants of human MetAP1b at low micromolar concentration. Molecular dynamics simulations suggest that ovalicin is not stably placed in the active site of wild-type MetAP1b before the covalent modification. In the case of F309M mutant and human Type 2 MetAP, molecule spends more time in the active site providing time for covalent modification.

Efficient dehydrative alkylation of thiols with alcohols catalyzed by alkyl halides

2017 ◽  
Vol 15 (45) ◽  
pp. 9638-9642 ◽  
Author(s):  
Yaqi Yang ◽  
Zihang Ye ◽  
Xu Zhang ◽  
Yipeng Zhou ◽  
Xiantao Ma ◽  
...  
Keyword(s):  
Transition Metal ◽  
Alkyl Halide ◽  
Alkyl Halides ◽  
Alkylation Reaction

Alcohols can be efficiently converted into thioethers by a transition metal- and base-free alkyl halide-catalyzed S-alkylation reaction with thiols or disulfides.

scholarly journals Pd-Catalyzed Cross-Electrophile Coupling/C–H Alkylation Reaction Enabled by a Mediator Generated via C(sp3)–H Activation

2021 ◽  
Author(s):  
Zhuo Wu ◽  
Hang Jiang ◽  
Yanghui Zhang
Keyword(s):  
Transition Metal ◽  
Alkyl Group ◽  
Alkylation Reaction ◽  
Aromatic Rings ◽  
Transition Metal Catalyzed ◽  
Metal Catalyzed ◽  
Alkylation Reactions

Transition-metal-catalyzed cross-electrophile C(sp2)–(sp3) coupling and C–H alkylation reactions represent two efficient methods for the incorpration of an alkyl group into aromatic rings. Herein, we report a Pd-catalyzed cascade cross-electrophile coupling...

scholarly journals Kinetic and structural mechanism for DNA unwinding by a non-hexameric helicase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sean P. Carney ◽  
Wen Ma ◽  
Kevin D. Whitley ◽  
Haifeng Jia ◽  
Timothy M. Lohman ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
Atp Hydrolysis ◽  
Variable Number ◽  
Structural Basis ◽  
Variable Step Size ◽  
Dna Unwinding ◽  
Step Size ◽  
Structural Mechanism ◽  
Dynamics Simulations

AbstractUvrD, a model for non-hexameric Superfamily 1 helicases, utilizes ATP hydrolysis to translocate stepwise along single-stranded DNA and unwind the duplex. Previous estimates of its step size have been indirect, and a consensus on its stepping mechanism is lacking. To dissect the mechanism underlying DNA unwinding, we use optical tweezers to measure directly the stepping behavior of UvrD as it processes a DNA hairpin and show that UvrD exhibits a variable step size averaging ~3 base pairs. Analyzing stepping kinetics across ATP reveals the type and number of catalytic events that occur with different step sizes. These single-molecule data reveal a mechanism in which UvrD moves one base pair at a time but sequesters the nascent single strands, releasing them non-uniformly after a variable number of catalytic cycles. Molecular dynamics simulations point to a structural basis for this behavior, identifying the protein-DNA interactions responsible for strand sequestration. Based on structural and sequence alignment data, we propose that this stepping mechanism may be conserved among other non-hexameric helicases.

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