Achieving natural product synthesis and diversity via catalytic networking ex vivo

Recent studies on ex vivo synthesis of natural products reveal that even complex multistep pathways can be successfully reconstructed. Genetic engineering of such reconstituted pathways has already been used to generate ‘unnatural’ natural products related to the original compound. In the future, it may be possible to use these approaches to make natural products that are currently inaccessible to conventional synthesis.     

Understanding organic gas-phase anion molecule reactions

Although ionic reactions in the gas phase seem on the surface to be totally different from those in solution (e.g., they typically occur about 10(12) times more rapidly than their solution analogues and go about as fast at 10 K as they do at room temperature), they can, in fact, exhibit subtle steric, electronic, and isotopic effects. In this Perspective, we show how these differences arise, explain why gas-phase ion reactions can be both fast and selective, and discuss when they can and cannot be classified as "hot" reactions. We also give examples of the use of these reactions to devise new synthetic pathways, investigate reaction mechanisms, and generate important thermochemical data such as bond dissociation energies.     

Theoretical study of the mechanism generating azomethine ylide from formaldehyde and glycine

The mechanism to generate azomethine ylide from formaldehyde and glycine is systematically investigated. The density functional theory at the B3LYP/6-311++G(d,p) level is employed for both geometry optimization and single point energy calculation. Our results indicate that two possible pathways can lead to the generation of the carbinolamine intermediate with a favorable step-wise pathway. However, as for the step to form azomethine ylide, a concerted elimination of water and carbon dioxide is preferred. This calculation result is totally different from the widely accepted revised Rizzi mechanism.     

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations

An efficient method for the calculation of minimum free energy pathways and free energy profiles for conformational transitions is presented. Short restricted perturbation-targeted molecular dynamics trajectories are used to generate an approximate free energy surface. Approximate reaction pathways for the conformational change are constructed from one-dimensional line segments on this surface using a Monte Carlo optimization. Accurate free energy profiles are then determined along the pathways by means of one-dimensional adaptive umbrella sampling simulations. The method is illustrated by its application to the alanine "dipeptide." Due to the low computational cost and memory demands, the method is expected to be useful for the treatment of large biomolecular systems.     

Mechanisms of water oxidation catalyzed by ruthenium diimine complexes

(18)O-isotope-labeling studies have led to the conclusion that there exist two major pathways for water oxidation catalyzed by dimeric ruthenium ions of the general type cis, cis-[L2Ru(III)(OH2)]2O(4+). We have proposed that both pathways involve concerted addition of H and OH fragments derived from H 2O to the complexes in their four-electron-oxidized states, i.e., [L2Ru(V)(O)]2O(4+), ultimately generating bound peroxy intermediates that decay with the evolution of O2. The pathways differ primarily in the site of addition of the OH fragment, which is either a ruthenyl O atom or a bipyridine ligand. In the former case, water addition is thought to give rise to a critical intermediate whose structure is L2Ru(IV)(OH)ORu(IV)(OOH)L2(4+); the structures of intermediates involved in the other pathway are less well defined but may involve bipyridine OH adducts of the type L2Ru(V)(O)ORu(IV)(OH)(L(*)OH)L(4+), which could react further to generate unstable dioxetanes or similar endoperoxides. Published experimental and theoretical support for these pathways is reviewed within the broader context of water oxidation catalysis and related reactions reported for other diruthenium and group 8 monomeric diimine-based catalysts. New experiments that are designed to probe the issue of bipyridine ligand "noninnocence" in catalysis are described. Specifically, the relative contributions of the two pathways have been shown to correlate with substituent effects in 4,4'- and 5,5'-substituted bipyridine complexes in a manner consistent with the formation of a reactive OH-adduct intermediate in one of the pathways, and the formation of OH-bipyridine adducts during catalytic turnover has been directly confirmed by optical spectroscopy. Finally, a photosensitized system for catalyzed water oxidation has been developed that allows assessment of the catalytic efficiencies of the complex ions under neutral and alkaline conditions; these studies show that the ions are far better catalysts than had previously been assumed based upon reported catalytic parameters obtained with strong oxidants in acidic media.     

Structure-based engineering of E. coli galactokinase as a first step toward in vivo glycorandomization

In vitro glycorandomization is a rapid chemoenzymatic strategy to diversify complex natural product scaffolds. The glycorandomization sugar activation pathway is dependent upon the efficient construction of diverse sugar-1-phosphate libraries. In the context of the previously evolved GalK Y371H "gatekeeper" mutation, the active site M173L mutation described herein presents a kinase with remarkably broadened substrate range to include 28 diverse natural and unnatural sugars. Among these new substrates, 6-azido-6-deoxy-galactose and 6-azido-6-deoxy-glucose present unique chemical probes to assess the utility of an E. coli Y371H/M173L-GalK-overproducing strain to generate unnatural sugar-1-phosphates in vivo. Remarkably, the in vivo conversion of both unnatural sugars rival that demonstrated in vitro. This notable in vivo success stands as the first step toward constructing short sugar-activation pathways in vivo and, ultimately, in vivo natural-product glycorandomization.     

Liquid chromatography–electrospray tandem mass spectrometry investigations of fragmentation pathways of biliary 4,4′-methylenedianiline conjugates produced in rats

4,4′-methylenedianiline (DAPM) is the main building block for production of 4,4′-methylenediphenyldiisocyanate that has been widely used in the manufacturing of polyurethane materials including medical devices. Although it was revealed that damage to biliary epithelial cells of the liver and common bile duct occurred upon acute exposure to DAPM, the exact mechanism of DAPM toxicity is not fully understood. Both phase I and II biotransformations of DAPM, some of which generate reactive intermediates, are characterized in detail by liquid chromatography electrospray tandem mass spectrometry. The two most prominent metabolites found in rat bile (M2 and M7) implicated glutathione, glucuronic acid, and glycine conjugations (phase II) following hydroxylation, and N-oxidation (phase I). Their decomposition pathways, as evidenced by MS ⁿ experiments, have been elucidated in detail. Figure Proposed fragmentation pathways of a DAPM metabolite     

Organic base effects in NHC promoted O- to C-carboxyl transfer; chemoselectivity profiles, mechanistic studies and domino catalysis

The O- to C-carboxyl transfer of oxazolyl carbonates promoted by triazolinylidenes, generated in situ with NEt(3), shows a markedly different rate and chemoselectivity profile to the same reaction promoted by triazolinylidenes generated using KHMDS. The mechanism of these pathways has been probed through extensive crossover studies to understand this process. The use of NEt(3) as a base allows domino multi-step reaction sequences to be developed, although chiral NHCs only generate modest levels of asymmetric induction (<15% ee) in these domino reaction processes.     

Synthesis and properties of azoles and their derivatives. 25. Electron-impact mass spectra of nitro- and nitroalkyl-substituted 3-aryl-δ2-isoxazolines

The fragmentation of nitro and nitroalkyl derivatives of 3-aryl-²-isoxazolines under the influence of electron impact was investigated. It was established that the fragmentation of the molecular ions of these compounds takes place primarily through the nitro- and halogen-containing groups; other pathways of dissociative ionization include the most important pathways of the fragmentation of arylisoxazoles.See [1] for Communication 24.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 7, pp. 980–983, July, 1990.     

Computational assessment of synthetic procedures

Synthetic chemistry is hard because some reasonable looking molecules cannot be made, because there are errors in the chemical literature, because it is easy to miss reaction possibilities and because even the shape of molecules is very difficult to determine. We propose an approach to the computational analysis of reactions that tries to circumvent these difficulties, by restricting the analysis to simple rules for reactivity that can generate a large number of competing pathways. This huge ensemble is filtered using computational methods to pick out the most likely pathways, and to suggest possible products.     

Roles of circadian clocks in cancer pathogenesis and treatment

Circadian clocks are ubiquitous timing mechanisms that generate approximately 24-h rhythms in cellular and bodily functions across nearly all living species. These internal clock systems enable living organisms to anticipate and respond to daily changes in their environment in a timely manner, optimizing temporal physiology and behaviors. Dysregulation of circadian rhythms by genetic and environmental risk factors increases susceptibility to multiple diseases, particularly cancers. A growing number of studies have revealed dynamic crosstalk between circadian clocks and cancer pathways, providing mechanistic insights into the therapeutic utility of circadian rhythms in cancer treatment. This review will discuss the roles of circadian rhythms in cancer pathogenesis, highlighting the recent advances in chronotherapeutic approaches for improved cancer treatment.Subject terms: Circadian rhythms, Targeted therapies     

The UPS: a promising target for breast cancer treatment

Abstract

During the past decade, progress in endocrine therapy and the use of trastuzumab has significantly contributed to the decline in breast cancer mortality for hormone receptor-positive and ERBB2 (HER2)-positive cases, respectively. As a result of these advances, a breast cancer cluster with poor prognosis that is negative for the estrogen receptor (ESR1), the progesterone receptor (PRGR) and ERBB2 (triple negative) has come to the forefront of medical therapeutic attention. DNA microarray analyses have revealed that this cluster is phenotypically most like the basal-like breast cancer that is caused by deficiencies in the BRCA1 pathways. To gain further improvements in breast cancer survival, new types of drugs might be required, and small molecules targeting the ubiquitin proteasome system have moved into the spotlight. The success of bortezomib in the treatment of multiple myeloma has sent encouraging signals that proteasome inhibitors could be used to treat other types of cancers. In addition, ubiquitin E3s involved in ESR1, ERBB2 or BRCA1 pathways could be ideal targets for therapeutic intervention. This review summarizes the ubiquitin proteasome pathways related to these proteins and discusses the possibility of new drugs for the treatment of breast cancers.

Publication history

Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com).

     

Current perspectives of <Superscript>14</Superscript>C-isotope measurement in biomedical accelerator mass spectrometry

Accelerator mass spectrometry (AMS) is an extremely sensitive nuclear physics technique developed in the mid-70s for radiocarbon dating of historical artefacts. The technique centres round the use of a tandem Van de Graaff accelerator to generate the potential energy to permit separation of elemental isotopes at the single atom level. AMS was first used in the early 90s for the analysis of biological samples containing enriched ¹⁴C for toxicology and cancer research. Since that time biomedical AMS has been used in the study of (1) metabolism of xenobiotics in animals and humans (2) pathways of drug metabolism (3) biomarkers (4) metabolism of endogenous molecules including vitamins (5) DNA and protein binding studies and (6) clinical diagnosis. A new drug development concept which relies on the ultrasensitivity of AMS known as human microdosing (Phase 0) is being used to obtain early human metabolism information of candidate drugs arising out of discovery. These various aspects of AMS are reviewed in this article and a perspective on future applications of AMS provided.     

Cleaning up our own backyard: developing new catabolic pathways to degrade pollutants

Microbial-based strategies for pollution control require metabolic pathways by which man-made compounds may be degraded. Recombination-based mutagenesis and selection procedures may be able to mimic the evolution of catabolic pathways and generate enzymes with novel specificities.     

Nanostructured Thermosetting Systems from Epoxidized Styrene Butadiene Block Copolymers

Summary: Nanostructured thermosetting materials were prepared by modification of an epoxy resin with 30 wt.‐% epoxidized polystyrene‐block‐polybutadiene copolymer (PS‐b‐PepB). The copolymer self‐assembles into a well‐defined hexagonal nanoordered structure, of around 30‐nm diameter, thus establishing its use as structure‐directing agent to generate nanostructured thermosetting materials. The study confirms pathways towards tailoring interactions between thermosetting matrices and immiscible block copolymers by using the concept of functionalization to build nanostructured polymer matrices.

Structure of diglycidyl ether of bisphenol‐A/4,4′‐methylenebis(3‐chloro 2,6‐diethylaniline) cured blend containing 30 wt.‐% PS‐b‐PepB61 block copolymer.     

Exploring new chemical space by stereocontrolled diversity-oriented synthesis

Natural products that act as highly specific, small-molecule protein-binding agents and as modulators of protein-protein interactions are highly complex and exhibit functional groups with three-dimensional and stereochemical diversity. The complex three-dimensional display of chiral functional groups appears to be crucial for exhibiting specificity in protein binding and in differentiating between closely related proteins. The development of methods that allow a high-throughput access to three-dimensional, skelatally complex, polycyclic compounds having few asymmetric diversity sites is essential and a highly challenging task. In the postgenomic chemical biology age, in which there is a great desire to understand protein-protein interactions and to dissect protein networking-based signaling pathways by small molecules, the need for developing "stereocontrolled, diversity-oriented synthesis" methods to generate natural product-like libraries is of utmost importance.     

Photodecomposition of substituted <Emphasis Type="Italic">o</Emphasis>-benzoquinones in saturated hydrocarbons: I. Kinetic relations

Kinetic relations holding in photodecomposition of substituted o-benzoquinones were determined, and primary photodecomposition products were identified. Photochemical transformations of o-benzoquinones in saturated hydrocarbons were presumed to follow two pathways: decarbonylation and reduction. The first of these is favored by the presence of electron-donor substituents in the quinoid ring.     

Mechanism of 1,3-dipolar cycloaddition reactions of indan-1-one enamines with aryl nitrile oxide: a DFT analysis

The mechanism (regioselectivity) of [3+2] cycloaddition reaction of indan-1-one enamines (1ad–1ce) with aryl nitrile oxide (2) has been investigated by density functional theory-based reactivity indices and activation energy calculations at B3LYP/6-31G(d) level of theory in the gas phase. Thermodynamic and kinetic parameters of the possible 3-regio/4-regio regioisomeric pathways have been determined. In all cases, the 3-regio pathways are more favorable compared to the 4-regio alternatives. Our results show that these cycloadditions follow an asynchronous one-step mechanism with a nonpolar character. Theoretical data are in good agreement with the experimental results.     

Density functional theory study of the regio‐ and stereoselectivity of 1,3-dipolar cycloaddition reactions between 2-ethylthio-4-phenyl-1-azetin and some substituted nitrile oxides

The mechanism (regio- and stereoselectivity) of 1,3-dipolar cycloaddition (1,3-DC) of 2-ethylthio-4-phenyl-1-azetin 1 with benzonitrile oxide 2a, 2-aminobenzonitrile oxide 2b and 2-azidobenzonitrile oxide 2c has been investigated by density functional theory-based reactivity indices and activation energy calculations at B3LYP/6-31G(d,p) level of theory in the gas and solvent phase. Thermodynamic and kinetic parameters of the possible ortho/meta regioisomeric and endo/exo stereoisomeric pathways have been determined. In order to rationalize complete endo selective fashion provided by these 1,3-DC cycloadditions, a natural steric analysis between NLMOs i,j for TS1ox and TS1on and also a second-order interaction energy, E ², analysis between the donor–acceptor orbitals in these TSs were carried out. In all cases, the ortho pathways are more favorable compared to the meta alternatives and it is found that the endo pathway is preferred. Our results show that these cycloadditions follow an asynchronous one-step mechanism with a nonpolar character. Theoretical data are in good agreement with the experimental results.     

Analysis of protein pathway networks using hybrid properties

Given a protein-forming system, i.e., a system consisting of certain number of different proteins, can it form a biologically meaningful pathway? This is a fundamental problem in systems biology and proteomics. During the past decade, a vast amount of information on different organisms, at both the genetic and metabolic levels, has been accumulated and systematically stored in various specific databases, such as KEGG, ENZYME, BRENDA, EcoCyc and MetaCyc. These data have made it feasible to address such an essential problem. In this paper, we have analyzed known regulatory pathways in humans by extracting different (biological and graphic) features from each of the 17,069 protein-formed systems, of which 169 are positive pathways, i.e., known regulatory pathways taken from KEGG; while 16,900 were negative, i.e., not formed as a biologically meaningful pathway. Each of these protein-forming systems was represented by 352 features, of which 88 are graph features and 264 biological features. To analyze these features, the "Minimum Redundancy Maximum Relevance" and the "Incremental Feature Selection" techniques were utilized to select a set of 22 optimal features to query whether a protein-forming system is able to form a biologically meaningful pathway or not. It was found through cross-validation that the overall success rate thus obtained in identifying the positive pathways was 79.88%. It is anticipated that, this novel approach and encouraging result, although preliminary yet, may stimulate extensive investigations into this important topic.