Mutability-Landscape-Guided Engineering of l-Threonine Aldolase Revealing the Prelog Rule in Mediating Diastereoselectivity of C−C Bond Formation

l -threonine aldolase (LTA) catalyzes C−C bond synthesis with moderate diastereoselectivity. In this study, with LTA from Cellulosilyticum sp (CpLTA) as an object, a mutability landscape was first constructed by performing saturation mutagenesis at substrate access tunnel amino acids. The combinatorial active-site saturation test/iterative saturation mutation (CAST/ISM) strategy was then used to tune diastereoselectivity. As a result, the diastereoselectivity of mutant H305L/Y8H/V143R was improved from 37.2 %_syn to 99.4 %_syn. Furthermore, the diastereoselectivity of mutant H305Y/Y8I/W307E was inverted to 97.2 %_anti. Based on insight provided by molecular dynamics simulations and coevolution analysis, the Prelog rule was employed to illustrate the diastereoselectivity regulation mechanism of LTA, holding that the asymmetric formation of the C−C bond was caused by electrons attacking the carbonyl carbon atom of the substrate aldehyde from the re or si face. The study would be useful to expand LTA applications and guide engineering of other C−C bond-forming enzymes.     

Chemistry and Biology of the Clinically Used Macrolactone Antibiotic Fidaxomicin

Fidaxomicin ( 1 , lipiarmycin A3, clostomicin B1, tiacumicin B) constitutes a glycosylated 18-membered macrolactone and is a natural product isolated from various soil bacteria. Since 2011, fidaxomicin is a marketed antibiotic for the treatment of intestine infections caused by C. difficile in the clinic. Its promising in vitro antibacterial properties against resistant S. aureus and M. tuberculosis continue to attract interest. This review article describes the early history of the antibiotic fidaxomicin and highlights recent advances in the field, such as the elucidation of its mode of action and biosynthesis, as well as known derivatives. Furthermore, different synthetic strategies towards the total synthesis of fidaxomicin are summarized.     

Chemical synthesis of bacterial lipoteichoic acids: an insight on its biological significance

During infections caused by Gram-negative bacteria, lipopolysaccharide (LPS, endotoxin) has a dominant role leading to fulminant pro-inflammatory reactions in the host. As there is no LPS in Gram-positive bacteria, other microbial cell wall components have been identified to be the causative agent for the pro-inflammatory activity since also Gram-positive bacterial infections lead to comparable clinical symptoms and reactions. On search for the "Gram-positive endotoxin" a widely accepted hypothesis has been raised in that the lipoteichoic acids (LTAs) serve as pathogen-associated molecular patterns (PAMPs) during Gram-positive sepsis, although the amount necessary for a pro-inflammatory in vitro response is several orders of magnitude higher than that for LPS. Therefore, LTA cannot be considered to be "the (endo)toxin of Gram-positive bacteria". Although LPS and LTA show structural relatedness (amphiphilic, negatively charged glycophospholipids), they are structurally quite different from each other and one might expect that they are also recognized by different receptors of the innate immune system, the so called toll-like receptors 4 and 2 (TLR4 and TLR2), respectively. Based on their chemical structure, the LTAs were classified into four types (type I-IV) of which we have carefully investigated the LTA of Staphylococcus aureus (type I), Lactococcus garvieae (type II) and Streptococcus pneumoniae (type IV). Hence, these LTAs have been synthesized in our group and biologically evaluated with respect to their potency to activate cytokines in transiently TLR2/CD14-transfected human endothelial kidney cells (HEK 293) or human macrophages and whole blood cells. Although LTA of type I and IV are structurally quite different, especially in their hydrophilic moiety, they originally were believed to interact with the same receptor (TLR2). Hence, the chemical syntheses leading to structurally defined, non-contaminated stimuli have a major impact on the outcome and interpretation of these biological studies of the innate immune system. With this material, it became evident that synthetic LTA from S. aureus and S. pneumoniae are not recognized by TLR2. Instead, another receptor of the innate immune system, the lectin pathway of the complement, known since many years to interact with LTA in quite a specific way, has gained increasing attractivity. With the help of synthetic LTA we obtained first evidences that this receptor is indeed the pathogen recognition receptor (PRR) for LTA.     

Total Synthesis of the Protected Aglycon of Fidaxomicin (Tiacumicin B,Lipiarmycin A3)

Fidaxomicin, also known as tiacumicin B or lipiarmycin A3, is a novel macrocyclic antibiotic that is used in hospitals for the treatment of Clostridium difficile infections. This natural product has also been shown to have excellent bactericidal activity against multidrug‐resistant Mycobacterium tuberculosis. In spite of its attractive biological activity, no total synthesis has been reported to date. The enantioselective synthesis of the central 18‐membered macrolactone is reported herein. The key reactions include ring‐closing metathesis between a terminal olefin and a dienoate moiety for macrocyclization, a vinylogous Mukaiyama aldol reaction, and a Stille coupling reaction of sterically demanding substrates. The retrosynthesis involves three medium‐sized fragments, thus leading to a flexible yet convergent synthetic route.     

Asymmetric Total Synthesis of Cytotrienin A: Late-Stage Installation of C11 Side Chain onto the Macrolactam Scaffold

Cytotrienin A, an ansamycin-class antibiotic, exhibits potent apoptosis-inducing activity and has attracted much attention as a lead compound for anticancer drugs. Herein, we report a new asymmetric synthetic route to cytotrienin A, employing an unexplored approach involving the late-stage installation of a C11 side chain onto the macrolactam core. In this strategy, we utilized the redox properties of hydroquinone and installed a side chain on the sterically hindered C11 hydroxy group by the traceless Staudinger reaction. This study also demonstrated that the boron-Wittig/iterative Suzuki–Miyaura cross-coupling sequence was effective for the concise and selective construction of the (E,E,E)-conjugated triene moiety. The developed route opens new opportunities for the structure–activity relationship studies of the side chains of these ansamycin antibiotics and the preparation of other synthetic analogs and chemical probes for further biological studies.     

Synthesis of the core structure of the lipoteichoic acid of Streptococcus pneumoniae

Streptococcus pneumoniae LTA is a highly complex glycophospholipid that consists of nine carbohydrate residues: three glucose, two galactosamine and two 2‐acetamino‐4‐amino‐2,4,6‐trideoxygalactose (AATDgal) residues that are each differently linked, one ribitol and one diacylated glycerol (DAG) residue. Suitable building blocks for the glucose and the AATDgal residues were designed and their synthesis is described in this paper. These building blocks permitted the successful synthesis of the core structure Glcβ(1‐3)AATDgalβ(1‐3)Glcα(1‐O)DAG in a suitably protected form for further chain extension ( 1 b , 1 c ) and as unprotected glycolipid ( 1 a ) that was employed in biological studies. These studies revealed that 1 a as well as 1 lead to interleukin‐8 release, however not via TLR2 or TLR4 as receptor.     

Improving the Cβ Stereoselectivity of l-Threonine Aldolase for the Synthesis of l-threo-4-Methylsulfonylphenylserine by Modulating the Substrate-Binding Pocket To Control the Orientation of the Substrate Entrance

l -Threonine aldolase from Actinocorallia herbida (AhLTA) is an ideal catalyst for producing l -threo-4-methylsulfonylphenylserine [(2S,3R)- 1 b ], a key chiral precursor for florfenicol and thiamphenicol. The moderate C_β stereoselectivity is the main obstacle to the industrial application of AhLTA. To address this issue, a combinatorial active-site saturation test (CAST) together with sequence conservatism analysis was applied to engineer the AhLTA toward improved C_β stereoselectivity. The optical mutant Y314R could asymmetrically synthesize l -threo-4-methylsulfonylphenylserine with 81 % diastereomeric excess (de), which is 23 % higher than wild-type AhLTA. Molecular dynamic (MD) simulations revealed that the mechanism for the improvement in C_β stereoselectivity of Y314R is due to the acylamino group of residues Arg314 controlling the orientation of substrate 4-methylsulfonyl benzaldehyde ( 1 a ) in the active pocket by directed interaction with the methylsulfonyl group; this leads to asymmetric synthesis of l -threo-4-methylsulfonylphenylserine. The success in this study demonstrates that direct control of substrates in an active pocket is an attract strategy to address the C_β stereoselectivity problem of LTA and contribute to the industrial application of LTA.     

Protein purification by aminosquarylium cyanine dye‐affinity chromatography

The most selective purification method for proteins and other biomolecules is affinity chromatography. This method is based on the unique biological‐based specificity of the biomolecule–ligand interaction and commonly uses biological ligands. However, these ligands may present some drawbacks, mainly because of their cost and lability. Dye‐affinity chromatography overcomes the limitations of biological ligands and is widely used owing to the low cost of synthetic dyes and to their resistance to biological and chemical degradation. In this work, immobilized aminosquarylium cyanine dyes are used in order to exploit affinity interactions with standard proteins such as lysozyme, α‐chymotrypsin and trypsin. These studies evaluate the affinity interactions occurring between the immobilized ligand and the different proteins, as a reflection of the sum of several molecular interactions, namely ionic, hydrophobic and van der Waals, spread throughout the structure, in a defined spatial manner. The results show the possibility of using an aminosquarylium cyanine dye bearing a N‐hexyl pendant chain, with a ligand density of 1.8 × 10^?2 mmol of dye/g of chromatographic support, to isolate lysozyme, α‐chymotrypsin and trypsin from a mixture. The application of a decreasing ammonium sulfate gradient resulted in the recovery of lysozyme in the flowthrough. On the other hand, α‐chymotrypsin and trypsin were retained, involving different interactions with the ligand. In conclusion, this study demonstrates the potential applicability of ligands such as aminosquarylium cyanine dyes for the separation and purification of proteins by affinity chromatography. Copyright © 2013 John Wiley & Sons, Ltd.     

Synthesis and Prediction of the Ubiquinol‐cytochrome c Reductase Inhibitory Activity of 3,4‐Dihydroisoquinolines and 2‐Azaspiro[4.5]decanes (Spiropyrrolines)

Isoquinolines rank as the second largest group among the plant alkaloids. Natural isoquinolines and synthetic isoquinoline derivatives exhibit numerous biological activities. In this study, the approaches to synthesis of new 3,4‐dihydroisoquinoline and 2‐azaspiro[4.5]decane (spiropyrroline) derivatives annelated by C(3)─C(4) bonds with a cyclohexyl or cyclopentyl moiety have been developed. In accord with the results of biological activity prediction by the pass software, molecular docking was carried out on the ubiquinol‐cytochrome c reductase (bc₁ complex) model. Compounds 6e and 12a , d were found out as potential Q₀ site inhibitors of the bovine bc₁ complex.     

Revised Structure of Tolyporphin A

Four monocyclic precursors were assembled in the total synthesis of the proposed structure 1 - A of (+)-tolyporphin A O,O-diacetate (X=Ac). Comparison of the spectroscopic data demonstrated that synthetic tolyporphin O,O-diacetate did not match the O,O-diacetate prepared from natural (+)-tolyporphin A (X=H), calling for a structural revision of this class of natural products. On the basis of a series of NMR experiments including synthetic intermediates, the structure of tolyporphin A is concluded to be 1 - B , in which the configurations of quaternary centers C7 and C17 are opposite to those in the originally proposed structure.     

Total Synthesis of the Proposed Structure of (+)-Tolyporphin A O,O-Diacetate

Four monocyclic precursors were assembled in the total synthesis of the proposed structure 1 - A of (+)-tolyporphin A O,O-diacetate (X=Ac). Comparison of the spectroscopic data demonstrated that synthetic tolyporphin O,O-diacetate did not match the O,O-diacetate prepared from natural (+)-tolyporphin A (X=H), calling for a structural revision of this class of natural products. On the basis of a series of NMR experiments including synthetic intermediates, the structure of tolyporphin A is concluded to be 1 - B , in which the configurations of quaternary centers C7 and C17 are opposite to those in the originally proposed structure.     

Materials Discovery and Crystal Growth of Zeolite A Type Zeolitic–Imidazolate Frameworks Revealed by Atomic Force Microscopy

A new zeolitic–imidazolate framework (ZIF), [Zn(imidazolate)_2?x(benzimidazolate)_x], that has the zeolite A (LTA) framework topology and contains relatively inexpensive organic linkers has been revealed using in situ atomic force microscopy. The new material was grown on the structure‐directing surface of [Zn(imidazolate)_1.5(5‐chlorobenzimidazolate)_0.5] (ZIF‐76) crystals, a metal–organic framework (MOF) that also possesses the LTA framework topology. The crystal growth processes for both [Zn(imidazolate)_2?x(benzimidazolate)_x] and ZIF‐76 were observed using in situ atomic force microscopy; it is the first time the growth process of a nanoporous material with the complex zeolite A (LTA) framework topology has been monitored temporally at the nanoscale. The results reveal the crystal growth mechanisms and possible surface terminations on the {100} and {111} facets of the materials under low supersaturation conditions. Surface growth of these structurally complex materials was found to proceed through both “birth‐and‐spread” and spiral crystal‐growth mechanisms, with the former occurring through the nucleation and spreading of metastable and stable sub‐layers reliant on the presence of non‐framework species to bridge the framework during formation. These results support the notion that the latter process may be a general mechanism of surface crystal growth applicable to numerous crystalline nanoporous materials of differing complexity and demonstrate that the methodology of seeded crystal growth can be used to discover previously unobtainable ZIFs and MOFs with desirable framework compositions.     

Total Synthesis of a Hyperbranched N‐Linked Hexasaccharide Attached to ATCV‐1 Major Capsid Protein without Precedent

The N‐glycans attached to some chloroviruses comprise a hyperbranched core structure without precedent. We are interested in the chemical synthesis of the hexasaccharide attached to ATCV‐1 (Acanthocystis turfacea Chlorella virus 1) for its distinct structure. After exploring four routes, the target hexasaccharide 2 was successfully synthesized for the first time in overall 10% yield over 8 steps from thioglycoside building blocks. This synthetic protocol is characterized by the three‐component one‐pot glycosylation and the regioselective glycosylation reactions. The disclosed synthetic approach to this new type of N‐glycans will facilitate the in‐depth understanding of their biological functions.     

Imidazolinium-based Multiblock Amphiphile as Transmembrane Anion Transporter

Transmembrane anion transport is an important biological process in maintaining cellular functions. Thus, synthetic anion transporters are widely developed for their biological applications. Imidazolinium was introduced as anion recognition site to a multiblock amphiphilic structure that consists of octa(ethylene glycol) and aromatic units. Ion transport assay using halide-sensitive lucigenin and pH-sensitive 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) revealed that imidazolinium-based multiblock amphiphile ( IMA ) transports anions and showed high selectivity for nitrate, which plays crucial roles in many biological events. Temperature-dependent ion transport assay using 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) indicated that IMA works as a mobile carrier. ¹H NMR titration experiments indicated that the C2 proton of the imidazolinium ring recognizes anions via a (C−H)⁺⋅⋅⋅X⁻ hydrogen bond. Furthermore, all-atom molecular dynamics simulations revealed a dynamic feature of IMA within the membranes during ion transportation.     

In Vitro Selection of a DNA Aptamer Targeting Degraded Protein Fragments for Biosensing

Protein biomarkers often exist as degradation fragments in biological samples, and affinity agents derived using a purified protein may not recognize them, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by selecting aptamers against a degraded form of the toxin B protein, which is a marker for diagnosing toxigenic Clostridium difficile infections. This approach has led to isolation of a DNA aptamer that recognizes degraded toxin B, fresh toxin B, and toxin B spiked into human stool samples. DNA aptamers selected using intact recombinant toxin B failed to recognize degraded toxin B, which is the form present in stored stool samples. Using this new aptamer, we produced a simple paper‐based analytical device for colorimetric detection of toxin B in stool samples, or in the NAP1 strain of Clostridium difficile. The combined aptamer‐selection and paper‐sensing strategy can expand the practical utility of DNA aptamers in clinical diagnosis.     

In Vitro Selection of a DNA Aptamer Targeting Degraded Protein Fragments for Biosensing

Protein biomarkers often exist as degradation fragments in biological samples, and affinity agents derived using a purified protein may not recognize them, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by selecting aptamers against a degraded form of the toxin B protein, which is a marker for diagnosing toxigenic Clostridium difficile infections. This approach has led to isolation of a DNA aptamer that recognizes degraded toxin B, fresh toxin B, and toxin B spiked into human stool samples. DNA aptamers selected using intact recombinant toxin B failed to recognize degraded toxin B, which is the form present in stored stool samples. Using this new aptamer, we produced a simple paper-based analytical device for colorimetric detection of toxin B in stool samples, or in the NAP1 strain of Clostridium difficile. The combined aptamer-selection and paper-sensing strategy can expand the practical utility of DNA aptamers in clinical diagnosis.     

Formation of Nanographite Using GaPO4-LTA as Template

An attempt was made to prepare nanographite with uniform size by pyrolysis of 4-methyl pyridine (MPy), which is the structure-directing agent for the formation of GaPO4-LTA single crystals, in the GaPO4-LTA framework at 760 ℃. The as-prepared nanographite has been examined by Raman spectroscopy, transmission electron microscopy (TEM), electron spin resonance (ESR) and magnetization characterizations. The TEM image shows that the size of individual nanographite particles is about 7 nm, and it is proved that there are spins of sp^2-type (π-type) radical electrons localized on the zigzag edge sites of the nanographite. The magnetic susceptibility of the nanographite shows crossover from a high-temperature diamagnetic to a low-temperature paramagnetic behavior, in good agreement with the theoretical expectation.     

δ13C, δ15N and δ2H isotope ratio mass spectrometry of ephedrine and pseudoephedrine: application to methylamphetamine profiling

Conventional chemical profiling of methylamphetamine has been used for many years to determine the synthetic route employed and where possible to identify the precursor chemicals used. In this study stable isotope ratio analysis was investigated as a means of determining the origin of the methylamphetamine precursors, ephedrine and pseudoephedrine. Ephedrine and pseudoephedrine may be prepared industrially by several routes. Results are presented for the stable isotope ratios of carbon (δ¹³C), nitrogen (δ¹⁵N) and hydrogen (δ²H) measured in methylamphetamine samples synthesized from ephedrine and pseudoephedrine of known provenance. It is clear from the results that measurement of the δ¹³C, δ¹⁵N and δ²H stable isotope ratios by elemental analyzer/thermal conversion isotope ratio mass spectrometry (EA/TC‐IRMS) in high‐purity methylamphetamine samples will allow determination of the synthetic source of the ephedrine or pseudoephedrine precursor as being either of a natural, semi‐synthetic, or fully synthetic origin. Copyright © 2009 Commonwealth of Australia. Published by John Wiley & Sons, Ltd.     

Single-Crystal X-Ray Diffraction Studies of Oligonucleotides and Oligonucleotide–Drug Complexes

Nucleic acids constitute the library of genetic information for all living organisms. They also play a regulatory role in many biological events concerned with the utilization of genetic information. The double-helical model of DNA, proposed by Watson and Crick in 1953, suggested the structural basis for its biological role, but this insight into nucleic acid structures seems to have generated as many questions as it has provided answers. Experimental studies, in particular fiber diffraction work, yielded a wealth of information on the conformational flexibility of nucleic acids and on the importance of interactions with water and cations. Major advances in synthetic organic chemistry, with implications for molecular biology, propelled nucleic acid research forward in the late 1970s. The availability of milligram quantities of synthetic oligonucleotides of defined sequence and high purity paved the way for detailed and accurate structural analysis using single-crystal X-ray diffraction methods and, in more recent times, NMR spectroscopy. This article is a detailed survey of the structural results generated by crystallographic techniques as applied to DNA, RNA, and nucleic acid–drug complexes over the period 1979–1990. The appendix lists important definitions used in the characterization of oligonucleotide structures.