ABSTRACT
Lignin valorization is being intensely pursued via tandem catalytic depolymerization and biological funneling to produce single products. In many lignin depolymerization processes, aromatic dimers and oligomers linked by carbon-carbon bonds remain intact, necessitating the development of enzymes capable of cleaving these compounds to monomers. Recently, the catabolism of erythro-1,2-diguaiacylpropane-1,3-diol (erythro-DGPD), a ring-opened lignin-derived ß-1 dimer, was reported in Novosphingobium aromaticivorans. The first enzyme in this pathway, LdpA (formerly LsdE), is a member of the nuclear transport factor 2 (NTF-2)-like structural superfamily that converts erythro-DGPD to lignostilbene through a heretofore unknown mechanism. In this study, we performed biochemical, structural, and mechanistic characterization of the N. aromaticivorans LdpA and another homolog identified in Sphingobium sp. SYK-6, for which activity was confirmed in vivo. For both enzymes, we first demonstrated that formaldehyde is the C1 reaction product, and we further demonstrated that both enantiomers of erythro-DGPD were transformed simultaneously, suggesting that LdpA, while diastereomerically specific, lacks enantioselectivity. We also show that LdpA is subject to a severe competitive product inhibition by lignostilbene. Three-dimensional structures of LdpA were determined using X-ray crystallography, including substrate-bound complexes, revealing several residues that were shown to be catalytically essential. We used density functional theory to validate a proposed mechanism that proceeds via dehydroxylation and formation of a quinone methide intermediate that serves as an electron sink for the ensuing deformylation. Overall, this study expands the range of chemistry catalyzed by the NTF-2-like protein family to a prevalent lignin dimer through a cofactorless deformylation reaction.
Subject(s)
Lyases , Lignin/metabolism , Bacterial Proteins/metabolism , Oxidoreductases/metabolism , StereoisomerismABSTRACT
α,ß-Diamino acids are important structural motifs and building blocks for numerous bioactive natural products, peptidomimetics, and pharmaceuticals, yet efficient asymmetric synthesis to access these stereoarrays remains a challenge. Herein, we report the development of a pyridoxal 5'-phosphate (PLP)-dependent enzyme that is engineered to catalyze stereoselective Mannich-type reactions between free α-amino acids and enolizable cyclic imines. This biocatalyst enabled one-step asymmetric enzymatic synthesis of the unusual pyrrolidine-containing amino acid L-tambroline at gram-scale with high enantio- and diastereocontrol. Furthermore, this enzymatic platform is capable of utilizing a diverse range of α-amino acids as the Mannich donor and various cyclic imines as the acceptor. By coupling with different imine-generating enzymes, we established versatile biocatalytic cascades and demonstrated a general, concise, versatile, and atom-economic approach to access unprotected α,ß-diamino acids, including structurally complex α,α-disubstituted α,ß-diamino acids with contiguous stereocenters.
Subject(s)
Amino Acids , Imines , Imines/chemistry , Imines/metabolism , Stereoisomerism , Amino Acids/chemistry , Amino Acids/chemical synthesis , Amino Acids/metabolism , Biocatalysis , Pyridoxal Phosphate/chemistry , Pyridoxal Phosphate/metabolism , Molecular StructureABSTRACT
Pyridoxal 5'-phosphate (PLP)-dependent enzymes that catalyze γ-replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP-dependent enzymes, CndF and Fub7, has unveiled unique C-C bond forming capabilities, enabling the biocatalytic synthesis of alkyl- substituted pipecolic acids from O-acetyl-L-homoserine and ß-keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone-derived enolates as carbon nucleophiles, revealing Fub7's capacity for substrate-dependent regioselective α-alkylation of unsymmetrical ketones. Through an integrated approach combining X-ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.
Subject(s)
Amino Acids , Pyridoxal Phosphate , Pyridoxal Phosphate/chemistry , Pyridoxal Phosphate/metabolism , Crystallography, X-Ray , Substrate Specificity , Carbon , CatalysisABSTRACT
An ambimodal transition state (TS) that leads to formation of four different pericyclic reaction products ([4 + 6]-, [2 + 8]-, [8 + 2]-, and [6 + 4]-cycloadducts) without any intervening minima has been designed and explored with DFT computations and quasiclassical molecular dynamics. Direct dynamics simulations propagated from the ambimodal TS show the evolution of trajectories to give the four cycloadducts. The topography of the PES is a key factor in product selectivity. A good correlation is observed between geometrical resemblance of the products to the ambimodal TS (measured by the RMSD) and the ratio of products formed in the dynamics simulations.
ABSTRACT
Four new PKS-NRPS-derived macrolide lactams with three unique ring fusion types were discovered from the Arctic sponge associated actinomycete Streptomyces somaliensis 1107 using a genome mining strategy. Their structures were elucidated by a combination of MS, NMR spectroscopic analysis, and single-crystal X-ray diffraction. Biosynthetically, a novel gene cluster sml consisting of three polyketide synthases and one hybrid polyketide synthase-nonribosomal peptide synthetase together with cytochrome P450s and flavin-containing monooxygenases and oxidoreductases was demonstrated to assemble the unique skeleton. Pharmacological studies revealed that compound 1 displayed a potent anti-inflammatory effect without cytotoxicity. It inhibited IL-6 and TNF-α release in the serum of LPS-stimulated RAW264.7 macrophage cells with IC50 values of 5.76 and 0.18â µM, respectively, and modulated the MAPK pathway. Moreover, compound 1 alleviated LPS-induced systemic inflammation in our transgenic fluorescent zebrafish model.
Subject(s)
Lactams , Macrolides , Animals , Macrolides/pharmacology , Lactams/pharmacology , Lipopolysaccharides/pharmacology , Zebrafish/metabolism , Anti-Bacterial Agents , Polyketide Synthases/metabolism , Anti-Inflammatory Agents/pharmacology , Peptide Synthases/metabolism , Multigene FamilyABSTRACT
The biosynthesis of pyrroindomycins A and B features a complexity-building [4 + 2] cycloaddition cascade, which generates the spirotetramate core under the catalytic effects of monofunctional Diels-Alderases PyrE3 and PyrI4. We recently showed that the main functions of PyrI4 include acid catalysis and induced-fit/conformational selection. We now present quantum mechanical and molecular dynamics studies implicating a different mode of action by PyrE3, which prearranges an anionic polyene substrate into a high-energy reactive conformation at which an inverse-electron-demand Diels-Alder reaction can occur with a low barrier. Stereoselection is realized by strong binding interactions at the endo stereochemical relationship and a local steric constraint on the endo-1,3-diene unit. These findings, illustrating distinct mechanisms for PyrE3 and PyrI4, highlight how nature has evolved multiple ways to catalyze Diels-Alder reactions.
Subject(s)
Molecular Dynamics Simulation , Catalysis , Cycloaddition Reaction , Molecular ConformationABSTRACT
Two new lactone lipids, scoriosin (1) and its methyl ester (2), with a rare furylidene ring joined to a tetrahydrofurandione ring, were isolated from Scorias spongiosa, commonly referred to as sooty mold. The planar structure of these compounds was assigned by 1D and 2D NMR. The conformational analysis of these molecules was undertaken to evaluate the relative and absolute configuration through GIAO NMR chemical shift analysis and ECD calculation. In addition to the potent antimicrobial activities, compound 2 strongly potentiated the activity of amphotericin B against Cryptococcus neoformans, suggesting the potential utility of this compound in combination therapies for treating cryptococcal infections.
Subject(s)
Anti-Infective Agents , Cryptococcus neoformans , Antifungal Agents/pharmacology , Ascomycota , Lactones/pharmacology , Lipids , Molecular StructureABSTRACT
The mechanism and dynamics for the formation of the delitschiapyrone family of natural products are studied by density functional theory (DFT) calculations and quasiclassical molecular dynamics simulations with DFT and xTB. In the uncatalyzed reaction, delitschiapyrones A and B are formed by Diels-Alder reactions through a single transition state and a post-transition state bifurcation that favors formation of delitschiapyrone B. In water and most likely in the enzyme, the acidic hydroxyquinone ionizes, and the resulting conjugate base undergoes cycloaddition preferentially to delitschiapyrone A. We demonstrate a new type of biosynthetic transformation and variable selectivity from a (4 + 2)/(4 + 3) ambimodal transition state.
Subject(s)
Biological Products , Naphthalenes , Pyrones , Toluene , Water , Biological Products/chemical synthesis , Biological Products/chemistry , Cycloaddition Reaction , Density Functional Theory , Molecular Dynamics Simulation , Molecular Structure , Naphthalenes/chemical synthesis , Naphthalenes/chemistry , Pyrones/chemical synthesis , Pyrones/chemistry , Solvents/chemistry , Toluene/chemistry , Water/chemistryABSTRACT
Monoterpene indole alkaloids are a large class of natural products derived from a single biosynthetic precursor, strictosidine. We describe a synthetic approach to strictosidine that relies on a key facially selective Diels-Alder reaction between a glucosyl-modified alkene and an enal to set the C15-C20-C21 stereotriad. DFT calculations were used to examine the origin of stereoselectivity in this key step, wherein two of 16 possible isomers are predominantly formed. These calculations suggest the presence of a glucosyl unit, also inherent in the strictosidine structure, guides diastereoselectivity, with the reactive conformation of the vinyl glycoside dienophile being controlled by an exo-anomeric effect. (-)-Strictosidine was subsequently accessed using late-stage synthetic manipulations and an enzymatic Pictet-Spengler reaction. Several new natural product analogs were also accessed, including precursors to two unusual aryne natural product derivatives termed "strictosidyne" and "strictosamidyne". These studies provide a strategy for accessing glycosylic natural products and a new platform to access monoterpene indole alkaloids and their derivatives.
Subject(s)
Alkynes/chemistry , Biological Products/chemistry , Vinca Alkaloids/chemical synthesis , Molecular Structure , Stereoisomerism , Vinca Alkaloids/chemistryABSTRACT
Here we report a nonenzymatic glycosylation reaction that builds axial S-glycosidic bonds under biorelevant conditions. This strategy is enabled by the design and use of allyl glycosyl sulfones as precursors to glycosyl radicals and exploits the exceptional functional group tolerance of radical processes. Our method introduces a variety of unprotected glycosyl units to the cysteine residues of peptides in a highly selective fashion. Through developing the second-generation protocol, we applied our method in the direct glycosylation of complex polypeptides and proteins. Computational studies were performed to elucidate the reaction mechanism.
Subject(s)
Peptides/chemical synthesis , Proteins/chemical synthesis , Glycosylation , Molecular Structure , Peptides/chemistry , Proteins/chemistry , StereoisomerismABSTRACT
A late-stage photoisomerization/cyclization union tactic, in conjunction with Type I Anion Relay Chemistry (ARC), permits enantioselective total syntheses and then biological evaluation of (+)-peniciketals A and B. The photochemical protocol was further showcased by an efficient three-step construction of the architecturally complex polycyclic skeleton found in (-)-diocollettines A. The mechanism and diastereoselectivity of the photochemical protocol have also been explored by both experiment and density functional theory calculations.
Subject(s)
Cyclization , Anions , Molecular StructureABSTRACT
The mechanism of the redox-neutral organocatalytic Mitsunobu reaction, catalyzed by (2-hydroxybenzyl)diphenylphosphine oxide, reported by Denton et al., has been studied computationally with ωB97X-D density functional theory. We discovered that the nucleophilic substitution reaction between carboxylate and alkoxyphosphonium ions, to reform the phosphine oxide catalyst, is the rate-determining step of the overall process and is significantly accelerated compared with a general-acid-catalyzed SN2 reaction. The (2-hydroxybenzyl)diphenylphosphine oxide is regenerated and activated in every catalytic cycle via intramolecular dehydration/cyclization. We also designed several phosphine oxide catalysts that we predict to be more effective catalysts.
ABSTRACT
We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.
Subject(s)
Bacterial Proteins/metabolism , Biological Products/metabolism , Ligases/metabolism , Binding Sites , Biocatalysis , Biological Products/chemistry , Crystallography, X-Ray , Cycloaddition Reaction , Density Functional Theory , Macrolides/chemistry , Macrolides/metabolism , Molecular Docking Simulation , Stereoisomerism , Streptomyces/enzymologyABSTRACT
We report the genome-guided discovery of sungeidines, a class of microbial secondary metabolites with unique structural features. Despite evolutionary relationships with dynemicin-type enediynes, the sungeidines are produced by a biosynthetic gene cluster (BGC) that exhibits distinct differences from known enediyne BGCs. Our studies suggest that the sungeidines are assembled from two octaketide chains that are processed differently than those of the dynemicin-type enediynes. The biosynthesis also involves a unique activating sulfotransferase that promotes a dehydration reaction. The loss of genes, including a putative epoxidase gene, is likely to be the main cause of the divergence of the sungeidine pathway from other canonical enediyne pathways. The findings disclose the surprising evolvability of enediyne pathways and set the stage for characterizing the intriguing enzymatic steps in sungeidine biosynthesis.
Subject(s)
Biosynthetic Pathways , Enediynes/metabolism , Antibiotics, Antineoplastic/metabolism , Multigene FamilyABSTRACT
A phytochemical investigation of the MeOH extract of the leaves and twigs of Amentotaxus argotaenia, a relict vulnerable coniferous species endemic to China, led to the isolation and characterization of 35 diterpenoids/norditerpenoids. Twenty of these are new, including 11 ent-kaurane-type (amentotaxins C-M, 1-11, respectively), three icetexane-type [= 9(10â20)abeo-abietane-type (amentotaxins N-P, 12-14, respectively)], four ent-labdane-type (amentotaxins Q-T, 15-18, respectively), and two isopimarane-type [amentotaxins U (19) and V (20)] compounds. Their structures were elucidated on the basis of spectroscopic data, single-crystal X-ray diffraction, the modified Mosher's method, and electronic circular dichroism data analyses. Compounds 1-9 are rare 18-nor-ent-kaurane-type diterpenoids featuring a 4ß,19-epoxy ring. All the isolates were evaluated for their cytotoxic effects against a small panel of cultured human cancer cell lines (HeLa, A-549, MDA-MB-231, SKOV3, Huh-7, and HCT-116), and some of them exhibited cytotoxicities with IC50 values ranging from 1.5 to 10.0 µM.
Subject(s)
Antineoplastic Agents, Phytogenic/pharmacology , Diterpenes/chemistry , Diterpenes/pharmacology , Plant Leaves/chemistry , Taxaceae/chemistry , Cell Line, Tumor , Drug Screening Assays, Antitumor , Humans , Molecular Structure , Spectrum Analysis/methodsABSTRACT
A chemical modification study was conducted on the marine natural product aaptamine (1), isolated from the marine sponge Aaptos aaptos. Thirty new derivatives substituted by various aromatic rings at the 3- and 7-positions of aaptamine were prepared by bromination, followed by the Suzuki coupling reaction. Sixteen compounds displayed cytotoxicities to four cancer cell lines (IC50 < 10 µM). In particular, compound 5i demonstrated a significant antiproliferative effect on the extranodal natural killer/T-cell lymphoma (ENKT) cell line SNK-6 with an IC50 value of 0.6 µM. Additionally, compound 5i showed cytotoxicities to multiple lymphoma cell lines, including Ramos, Raji, WSU-DLCL2, and SU-DHL-4 cells.
Subject(s)
Antineoplastic Agents/therapeutic use , Killer Cells, Natural/immunology , Lymphoma, T-Cell/drug therapy , Naphthyridines/therapeutic use , Drug Screening Assays, Antitumor , Humans , Lymphoma, T-Cell/immunology , Lymphoma, T-Cell/pathology , Naphthyridines/chemistryABSTRACT
The (3+2) cycloadditions between electron-deficient Pd-oxyallyls and conjugated dienes have been investigated with density functional theory calculations. A stepwise mechanism with C-C bond formation occurring first is supported by computations. The key electron-withdrawing ester substituent on the Pd-oxyallyl species decreases the migratory insertion barrier by both lowering the LUMO energy and enabling a less-strained six-membered coordination mode. The lack of (3+2) reactivity with monoenes is attributed to higher migratory insertion barriers due to a lower-energy HOMO, as well as high C-O reductive elimination barriers, which become rate-determining. Conjugated dienes enable the formation of a highly electrophilic η3 Pd-allyl species and greatly facilitates C-O formation.
ABSTRACT
We report here the orchestration of molecular ion networking and a set of computationally assisted structural elucidation approaches in the discovery of a new class of pyrroloiminoquinone alkaloids that possess selective bioactivity against pancreatic cancer cell lines. Aleutianamine represents the first in a new class of pyrroloiminoquinone alkaloids possessing a highly strained multibridged ring system, discovered from Latrunculia ( Latrunculia) austini Samaai, Kelly & Gibbons, 2006 (class Demospongiae, order Poecilosclerida, family Latrunculiidae) recovered during a NOAA deep-water exploration of the Aleutian Islands. The molecule was identified with the guidance of mass spectrometry, nuclear magnetic resonance, and molecular ion networking (MoIN) analysis. The structure of aleutianamine was determined using extensive spectroscopic analysis in conjunction with computationally assisted quantifiable structure elucidation tools. Aleutianamine exhibited potent and selective cytotoxicity toward solid tumor cell lines including pancreatic cancer (PANC-1) with an IC50 of 25 nM and colon cancer (HCT-116) with an IC50 of 1 µM, and represents a potent and selective candidate for advanced preclinical studies.
Subject(s)
Antineoplastic Agents/pharmacology , Indole Alkaloids/pharmacology , Alaska , Animals , Antineoplastic Agents/chemistry , Antineoplastic Agents/isolation & purification , Cell Line, Tumor , Drug Discovery , Humans , Indole Alkaloids/chemistry , Indole Alkaloids/isolation & purification , Mice , Models, Chemical , Molecular Structure , Porifera/chemistry , StereoisomerismABSTRACT
A unified synthetic strategy leading to the total synthesis of (-)-nodulisporic acids D, C, and B is described. Key synthetic transformations include a nickel-chromium-mediated cyclization, an aromatic ring functionalization employing a novel copper-promoted alkylation, a palladium-catalyzed cross-coupling cascade/indole ring construction, and a palladium-mediated regio- and diastereoselective allylic substitution/cyclization reaction, the latter to construct ring D.
Subject(s)
Indoles/chemical synthesis , Alkylation , Cyclization , Oxidation-Reduction , StereoisomerismABSTRACT
An effective late-stage large-fragment union/rearrangement exploiting the Petasis-Ferrier protocol, in conjunction with multicomponent Type I Anion Relay Chemistry (ARC) to access advanced intermediates, permits completion of a convergent, stereocontrolled total synthesis of the architecturally complex phosphomacrolide (-)-enigmazole A (1).