A unified synthetic approach to polyketides having both skeletal and stereochemical diversity

An efficient systematic approach to the diversity-oriented synthesis of polyketides has been developed to provide both skeletal and stereochemical diversity. Each synthetic intermediate is also a desired polyketide fragment and no protecting group manipulations are required. A first-generation synthesis provides a 74-membered polyketide library comprising six different skeletal classes, each in one to five steps from propargylic alcohol precursors. A study of epoxyol opening reactions revealed unusual reactivity trends based on epoxide configuration.     

Expanding stereochemical and skeletal diversity using petasis reactions and 1,3-dipolar cycloadditions

A short and modular synthetic pathway using intramolecular 1,3-dipolar cycloaddition reactions and yielding functionalized isoxazoles, isoxazolines, and isoxazolidines is described. The change in shape of previous compounds and those in this study is quantified and compared using principal moment-of-inertia shape analysis.     

Dissecting cellular processes using small molecules: identification of colchicine-like, taxol-like and other small molecules that perturb mitosis

BACKGROUND: Understanding the molecular mechanisms of complex cellular processes requires unbiased means to identify and to alter conditionally gene products that function in a pathway of interest. Although random mutagenesis and screening (forward genetics) provide a useful means to this end, the complexity of the genome, long generation time and redundancy of gene function have limited their use with mammalian systems. We sought to develop an analogous process using small molecules to modulate conditionally the function of proteins. We hoped to identify simultaneously small molecules that may serve as leads for the development of therapeutically useful agents. RESULTS: We report the results of a high-throughput, phenotype-based screen for identifying cell-permeable small molecules that affect mitosis of mammalian cells. The predominant class of compounds that emerged directly alters the stability of microtubules in the mitotic spindle. Although many of these compounds show the colchicine-like property of destabilizing microtubules, one member shows the taxol-like property of stabilizing microtubules. Another class of compounds alters chromosome segregation by novel mechanisms that do not involve direct interactions with microtubules. CONCLUSIONS: The identification of structurally diverse small molecules that affect the mammalian mitotic machinery from a large library of synthetic compounds illustrates the use of chemical genetics in dissecting an essential cellular pathway. This screen identified five compounds that affect mitosis without directly targeting microtubules. Understanding the mechanism of action of these compounds, along with future screening efforts, promises to help elucidate the molecular mechanisms involved in chromosome segregation during mitosis.     

Maximizing the stereochemical diversity of spiro-ladder oligomers

[reaction: see text] We introduce all stereoisomers of a bis-amino acid building block derived from trans-4-hydroxy-L-proline. This small library of monomers allows arbitrary stereochemical configuration at any chiral center within our spiro-ladder oligomers. Three tetramer oligomers containing several combinations of the monomers 1-4 were synthesized; we explored the effect of monomer sequence on scaffold conformation by NMR.     

A hydrodynamic approach to the measurement of the permeability of small molecules across artificial membranes

An in situ analytical approach to the measurement of supported liquid membrane permeability is reported. The method consists of a spectrophotometric method to measure transport through a membrane-supported lipid solution, using a rotating-diffusion cell configuration to overcome limits arising from transport through the aqueous solution boundary layer in stationary systems. Rotation frequencies are almost two orders of magnitude higher than those employed previously for rotating-diffusion studies of membrane transport. The method is illustrated with the transport of warfarin [1-(4'-hydroxy-3'-coumarinyl)-1-phenyl-3-butanone]. The use of the rotating-diffusion approach permits accurate calculation of the aqueous phase boundary layer thickness, which has hitherto been treated as an adjustable parameter in studies of membrane permeability. Further, it is shown that the analyte diffusion coefficient can be determined readily using liquid-liquid electrochemistry.     

Discovery of benthol A and its challenging stereochemical assignment: opening up a new window for skeletal diversity of super-carbon-chain compounds

Super-carbon-chain compounds (SCCCs) are marine organic molecules featuring long polyol carbon chains with numerous stereocenters. Polyol–polyene compounds (PPCs) and ladder-frame polyethers (LFPs) are two major families. It is highly challenging to establish the absolute configurations of SCCCs. In this century, few new SCCC families have been reported. Benthol A, an aberrant SCCC, was obtained from a South China Sea benthic dinoflagellate that should belong to a new taxon. Its planar structure and absolute configuration, containing thirty-five carbon stereocenters, were unambiguously established by a combination of extensive NMR spectroscopic investigations, periodate degradation of the 1,2-diol groups, ozonolysis of the carbon–carbon double bonds, J-based configurational analysis, NOE interactions, modified Mosher''s MTPA ester method, and DFT-NMR ¹³C chemical-shift calculations aided by DP4+ statistical analysis. Benthol A displayed potent antimalarial activity against Plasmodium falciparum 3D7 parasites. This new molecule combines extraordinary structural features, particularly eight scattered ether rings on a C₇₂ backbone chain, which places it within a new SCCC family between PPCs and LFPs, herein termed polyol–polyether compounds. This suggestion was strongly supported by principal component analysis. The discovery of benthol A does not only provide new insights into the untapped biosynthetic potential of marine dinoflagellates, but also opens up a new window for skeletal diversity of SCCCs.

The discovery of benthol A, a marine natural product featuring thirty-five carbon stereocenters and eight scattered ether rings within a C₇₂ backbone chain, inaugurates a new family of super-carbon-chain compounds.     

Identification of the cellular targets of bioactive small organic molecules using affinity reagents

The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cellular binding partners. Special emphasis is placed on logistical concerns as well as common problems encountered during such target identification experiments. The roadmap provided is a guide through the process of affinity probe selection, target identification, and downstream target validation.     

Intercomparison study on accurate mass measurement of small molecules in mass spectrometry

The results from an intercomparison of accurate mass measurement of a small molecule (molecular weight 475 Da) across a broad range of mass spectrometers are reported. The intercomparison was designed to evaluate the relative capabilities and the optimum methodology of the diverse range of mass spectrometers currently used to record accurate mass measurements. The data will be used as a basis for developing guidance on accurate mass measurement. The need for guidance has resulted from the continued growth in the use of accurate mass measurements for assignment of elemental formula in the chemical and biochemical industries. This has been fuelled by a number of factors and includes the rapid pace of instrument development, which has enabled accurate mass measurements to be made in a less costly, yet robust fashion. The data from the intercomparison will allow us to compare those protocols that produced excellent accuracy and precision with those that produced poorer accuracy and/or precision for each type of mass spectrometer. The key points for best practice will then be established from this comparison for each type of mass spectrometer and accurate mass measurement technique. A compound was sent to the participating laboratories (in the UK, Europe, and USA), the identity of which was not revealed. Each laboratory was asked to record a minimum of five repeat mass measurements of the molecular species using their local protocols and their preferred ionization technique or techniques. To the best of our knowledge there were no interfering (unresolved) ions that originated from the sample. A questionnaire was also completed with the experimental work. The information from the questionnaires was used to evaluate the protocols used to record the measurements. Forty-five laboratories have reported their results. To summarize the performance of mass spectrometers in the intercomparison, magnetic sector field mass spectrometers used in peak matching mode and FTMS reported the highest mean mass measurement accuracy (88 and 83%, respectively, achieved < or =1 ppm). Magnetic sector field mass spectrometers used in voltage scanning produced 60% of the mean mass measurements with accuracy < or =1 ppm. Magnetic sector field mass spectrometers used in magnet scanning modes, quadrupole-TOF and TOF instruments generally achieved mean mass measurement accuracy between 5 and 10 ppm. The two low resolution triple quadrupoles used in the inter-comparison produced mean mass measurement accuracy of <2 ppm. The precision of the data from each instrument and experiment type is an important consideration when evaluating their relative capabilities. Using both the precision and accuracy, it will be possible to define the uncertainty associated with the elemental formulae derived from accurate mass measurements. Therefore, a thorough statistical evaluation of the data is underway and will be presented in a subsequent publication.     

Application of gel chromatography to small molecules

Summary Liuid chromatographic separations of hydrocarbons, alcohols, triglycerides and surfactants with molecular weights ranging from 100–1,000 were accomplished, using columns packed with porous polymeric beads. The fractionation capability of the porous gels has been extended to smaller molecules through the development of small porosity gels. The gels separated according to molecular size and are therefore useful both for separation and identification purposes. Since they require no stationary liquid phase, they afford long column life without need of a saturated carrier.

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Zusammenfassung Flüssigkeits-chromatographische Trennungen von Kohlenwasserstoffen, Alkoholen, Triglyceriden und oberflächenaktiven Substanzen mit Molekulargewichten von 100–1000 wurden mit Hilfe von porösen Polymerkörnern erreicht. Das Trennvermögen der porösen Gele wurde durch Entwicklung kleinporiger Typen auf kleinere Moleküle ausgedehnt. Da die Moleküle entsprechend ihrer Größe getrennt werden, kann außer der Trennung auch eine Identifizierung erreicht werden. Da keine flüssige stationäre Phase erforderlich ist, ist eine lange Lebensdauer der Säulen gewährleistet.

     

A de novo approach to the synthesis of glycosylated methymycin analogues with structural and stereochemical diversity

A divergent and highly stereoselective route to 11 glycosylated methymycin analogues has been developed. The key to the success of this method was the iterative use of the Pd-catalyzed glycosylation reaction and postglycosylation transformation. This unique application of Pd-catalyzed glycosylation demonstrates the breath of α/β- and d/l-glycosylation of macrolides that can be efficiently prepared using a de novo asymmetric approach to the carbohydrate portion.     

Macrocycloadditions leading to conformationally restricted small molecules

[reaction: see text] The Cu(I)-catalyzed cycloaddition of alkynes and azides (click reaction) provides a robust method for the construction of macrocyclic small molecules via an intramolecular macrocycloaddition. A three-subunit system has been used to explore the tolerance of this macrocycloaddition to variations of stereochemistries and substituents.     

Binding of small guest molecules to multivalent receptors

The complexation of phenol derivatives, aromatic carboxylic acids, and n-octylgalactopyranoside by hydrogen-bonded exo-receptors is described. The receptors are formed by self-assembly of differently functionalized calix[4]arene dimelamines with 5,5-diethyl barbiturate or butyl cyanurate. The multivalent complementary recognition site of the receptors is used very efficiently to complex multiple guests. A 1:6 binding mode was observed for phenol derivatives forming single hydrogen bonds with all six recognition sites of an ureido functionalized receptor assembly, while 1:3 complexation was observed for phenol derivatives which form two hydrogen bonds with two different ureido recognition sites of the same receptor. Aromatic carboxylic acids are complexed in a 1:6 ratio by receptors having six amino recognition sites. The complexation of n-octylgalactopyranoside by Gly-L-Ser functionalized receptors is also described, indicating that it is possible to use small peptidic fragments to complex biologically important molecules.     

Stereochemical control of skeletal diversity

[reaction: see text]. Substrates having appendages that pre-encode skeletal information (sigma-elements) can be converted into products having distinct skeletons using a common set of reaction conditions. The sequential use of the Ugi 4CC-IMDA reaction, followed by allylation, hydrolysis, and acylation of a chiral amino alcohol appendage (sigma-element), leads to substrates for a ROM/RCM or RCM reaction. The stereochemistry of the sigma-element and not its constitution controls the outcome of the pathway selected. This work illustrates the potential of linking stereochemical control to the challenging problem of skeletal diversity.     

An oligomer-based approach to skeletal diversity in small-molecule synthesis

Access to small molecules of widely varying molecular shapes has been identified as an enabling step in the discovery of biologically active materials. In this communication we introduce an approach to the systematic development of architecturally distinct chemical compounds based upon the assembly of reactive monomers into linear oligomers, each of which encodes a unique molecular framework under a common set of reaction conditions. Certain products of the initial chemical transformation (Ru-catalyzed metathesis reaction) encode additional skeletons upon treatment with a second common set of reagents (Diels-Alder dienophiles). Application of this oligomerization approach has led to the discovery of a previously unreported tandem ene-yne-yne metathesis-6pi-electrocyclization-1,5-hydride migration that converts a linear substrate into a complex tricyclic 1,3-diene in a single step. Thus, the reported strategy might serve not only as a generator of skeletally diverse small molecules but also as a discovery platform for the identification of novel chemical transformations.     

Redox-active dinuclear macrocycles designed to bind and activate small molecules

The syntheses, electrochemistry and preliminary coordination studies of novel redox-active dinucleating macrocyclic molecules (FcCH₂SCH₂RCH₂SCH₂)₂ (Fc = ferrocenyl, R = CH₂SCH₂, NC₅H₃) and their acyclic analogues, which incorporate ferrocene subunits into cyclic and acyclic structural frameworks are described.     

Uranium-mediated activation of small molecules

Molecular complexes of uranium are capable of activating a range of industrially and economically important small molecules such as CO, CO(2), and N(2); new and often unexpected reactions provide insight into an element that needs to be well-understood if future clean-energy solutions are to involve nuclear power.     

A simple reaction to produce small structurally complex and diverse molecules

In order to mimic the complexity of natural products, we designed and obtained with simple synthetic methods, building blocks with `quaternary chiral centers'. These tricyclic lactams resulted from the reaction of a functional γ-keto-acid and various commercially available bi-nucleophiles.