Engineered biosynthesis of aklanonic acid analogues

Aklanonic acid, an anthraquinone natural product, is a common advanced intermediate in the biosynthesis of several antitumor polyketide antibiotics, including doxorubicin and aclacinomycin A. Intensive semisynthetic and biosynthetic efforts have been directed toward developing improved analogues of these clinically important compounds. The primer unit of such polyfunctional aromatic polyketides is an attractive site for introducing novel chemical functionality, and attempts have been made to modify the primer unit by precursor-directed biosynthesis or protein engineering of the polyketide synthase (PKS). We have previously demonstrated the feasibility of engineering bimodular aromatic PKSs capable of synthesizing unnatural hexaketides and octaketides. In this report, we extend this ability by preparing analogues of aklanonic acid, a decaketide, and its methyl ester. For example, by recombining the R1128 initiation module with the dodecaketide-specific pradimicin PKS, the isobutyryl-primed analogue of aklanonic acid (YT296b, 10) and its methyl ester (YT299b, 12) were prepared. In contrast, elongation modules from dodecaketide-specific spore pigment PKSs were unable to interact with the R1128 initiation module. Thus, in addition to revealing a practical route to new anthracycline antibiotics, we also observed a fundamental incompatibility between antibiotic and spore pigment biosynthesis in the actinomycetes bacteria.     

Role of local structure on motions on the potential energy landscape for a model supercooled polymer

We have conducted detailed Monte Carlo and molecular dynamics simulations of a model glass forming polymeric system near its apparent glass transition temperature. We have characterized the local structure of the glass using a Voronoi-Delaunay analysis of local particle arrangements. After a perturbative face elimination, we find that a significant fraction of Voronoi polyhedra consist of 12 pentagonal faces, a sign of icosahedral ordering. Further, we have identified metabasins of particle vibrations on the potential energy landscape on the basis of persistence of particle positions and neighbors over a simulated trajectory. We find that the residence times for vibrations are correlated with a particular Voronoi volume and number of neighbors of a particle; the largest metabasins correspond to particles whose average Voronoi volume is close to the value expected on the basis of the density, and whose approximate number of neighbors is close to 12. The local distortion around a particle, measured in terms of the tetrahedricity of the Delaunay simplices, reveals that the particles with a higher degree of local distortion are likely to transition faster to a neighboring metabasin. In addition to the transition between metabasins, we have also examined the influence of vibrations at inherent structures (IS) on the local structure, and find that the the low frequency modes at the IS exhibit the greatest curvature with respect to the local structure. We believe that these results establish an important connection between the local structure of glass formers and the activated dynamics, thereby providing insights into the origins of dynamic heterogeneities.     

Kinetics study of amine cleavage reactions of various resin-bound thiophenol esters from marshall linker

The kinetics of cleavage reactions of seven resin-bound thiophenol esters with three amines has been studied by single-bead FTIR. The reactivity of these seven thiophenol esters was dependent on their structures and could be summarized as follows: 5-benzimidazolecarboxylic thiophenol ester > alkyl thiophenol ester > aromatic thiophenol ester. The reactivity of three amines was summarized as follows: n-butylamine > 3,4-dimethoxyphenethylamine > 1-piperonylpiperazine. The rate of the cleavage reaction increased 2-fold per 10 degrees C rise in reaction temperature. Oxidation of the thiophenol linker increased the rate of the cleavage reaction by 580-fold.     

Self-assembly of diorganotin(IV) 2-{[(E)-1-(2-oxyaryl)alkylidene]amino}acetates: An investigation of structures by X-ray diffraction, solution and solid-state tin NMR, and electrospray ionization MS

The diorganotin(IV) compounds, [Me₂SnL²(OH₂)]₂ (1), [ⁿBu₂SnL²(OH₂)]₂ (2), [ⁿBu₂SnL¹]₃ · 0.5C₃H₆O (3), [ⁿBu₂SnL³]₃ · 0.5C₆H₆ (4) and [Ph₂SnL³]_n · 0.5C₆H₆ (5) (L = carboxylic acid residue, i.e., 2-{[(E)-1-(2-oxyaryl)alkylidene]amino}acetate), were synthesized by treating the appropriate diorganotin(IV) dichloride with the potassium salt of the ligand in anhydrous methanol.The reaction of Ph₂SnL² (L = 2-{[(E)-1-(2-oxyphenyl)ethylidene]amino}acetate) with 1,10-phenanthroline (Phen) yielded a 1:1 adduct of composition, [Ph₂SnL²(Phen)] (6).The crystal structures of 1-6 were determined.The crystal of 1 is composed of centrosymmetric dimers of the basic Me₂SnL²(OH₂) moiety, where the two Sn-centres are linked by two asymmetric Sn-O?Sn bridges involving the carboxylic acid O atom of the ligand and a long Sn?O distance of 3.174(2) Å.The dimers are further linked into columns by hydrogen bonds.The coordination geometry about the Sn atom is a distorted pentagonal bipyramid with the two methyl groups in axial positions.The structure of 2 is similar.The same Sn atom coordination geometry is observed in compound 3, which is a cyclic trinuclear[ⁿBu₂SnL¹]₃ compound. Each Sn atom is coordinated by the phenoxide O atom, one carboxylate O atom and the imino N atom from one ligand and both the exo- and endo-carboxylate O atoms (mean Sn-O(exo): 2.35 Å; Sn-O(endo): 2.96 Å) from an adjacent ligand to form the equatorial plane, while the two butyl groups occupy axial positions. Compound 4 was found to crystallize in two polymorphic forms. The Sn-complex in both forms has a trinuclear [ⁿBu₂SnL³]₃ structural motif similar to that found in 3. In compound 5, distorted trigonal bipyramidal Ph₂SnL³ units are linked into polymeric cis-bridged chains by a weak Sn?O interaction (3.491(2) Å) involving the exocyclic O atom of the tridentate ligand of a neighboring Sn-complex unit. This interaction completes a highly distorted octahedron about the Sn atom, where the weakly coordinated exocyclic O atom and one phenyl group are trans to one another. In contrast, a monomeric distorted pentagonal bipyramidal geometry is found for adduct 6 where the Sn-phenyl groups occupy the axial positions. The solution and solid-state structures are compared by using ¹¹⁹Sn NMR chemical shift data. Compounds 1-6 were also studied using ESI-MS and their positive- and negative-ions mass fragmentation patterns are discussed.     

Nanoswitches based on DNA base pairs: why adenine-thymine is less suitable than guanine-cytosine.

Substituted Watson–Crick guanine–cytosine (GC) base pairs were recently shown to yield robust three‐state nanoswitches. Here, we address the question: Can such supramolecular switches also be based on Watson–Crick adenine‐thymine (AT) base pairs? We have theoretically analyzed AT pairs in which purine‐C8 and/or pyrimidine‐C6 positions carry a substituent X=NH^?, NH₂, NH₃⁺ (N series), O^?, OH or OH₂⁺ (O series), using the generalized gradient approximation (GGA) of density functional theory at the BP86/TZ2P level. Thus, we explore the trend in geometrical shape and hydrogen bond strengths in AT pairs along a series of stepwise protonations of the substituents. Introducing a charge on the substituents leads to substantial and characteristic changes in the individual hydrogen bond lengths when compared to the neutral AT pair. However, the trends along the series of negative, neutral, and positive substituents are less systematic and less pronounced than for GC. In certain instances, internal proton transfer from thymine to adenine occurs. Our results suggest that AT is a less suitable candidate than GC in the quest for chemically controlled nanoswitches.     

Reconstitution and characterization of a new desosaminyl transferase, EryCIII, from the erythromycin biosynthetic pathway

EryCIII converts alpha-mycarosyl erythronolide B into erythromycin D using TDP-d-desosamine as the glycosyl donor. We report the heterologous expression, purification, in vitro reconstitution, and preliminary characterization of EryCIII. Coexpression of EryCIII with the GroEL/ES chaperone complex was found to enhance greatly the expression of soluble EryCIII protein. The enzyme was found to be highly active with a kcat greater than 100 min-1. EryCIII was quite selective for the natural nucleotide sugar donor and macrolide acceptor substrates, unlike several other antibiotic glycosyl transferases with broad specificity such as desVII, oleG2, and UrdGT2. Within detectable limits, neither 6-deoxyerythronolide B nor 10-deoxymethynolide were found to be glycosylated by EryCIII. Furthermore, TDP-d-mycaminose, which only differs from TDP-d-desosamine at the C4 position, could not be transferred to alphaMEB. These studies lay the groundwork for detailed structural and mechanistic analysis of an important member of the desosaminyl transferase family of enzymes.     

A Switch for the transfer of substrate between nonribosomal peptide and polyketide modules of the rifamycin synthetase assembly line

A nonribosomal peptide synthetase (NRPS) loading module and a polyketide synthase (PKS) elongation module catalyze the preliminary steps in the biosynthesis of the rifamycin antibiotics. A benzoate molecule is covalently attached to the phosphopantetheine arm of the thiolation domain of the loading module when its reaction partner methylmalonyl-CoA is absent. Occupancy of the thiolation domain of the elongation module by a methylmalonyl moiety appears to trigger intermodular transfer of benzoate to the ketosynthase domain of the elongation module. This transthiolation event is fast relative to the initial loading of benzoate onto the loading module. It will be of interest to determine if these results are generally true for intermodular acyl transfer in other NRPS-PKS and PKS assembly lines.     

The Power of Kinetic Inertness in Improving Platinum Anticancer Therapy by Circumventing Resistance and Ameliorating Nephrotoxicity

Even in the modern era of precision medicine and immunotherapy, chemotherapy with platinum (Pt) drugs remains among the most commonly prescribed medications against a variety of cancers. Unfortunately, the broad applicability of these blockbuster Pt drugs is severely limited by intrinsic and/or acquired resistance, and high systemic toxicity. Considering the strong interconnection between kinetic lability and undesired shortcomings of clinical Pt drugs, we rationally designed kinetically inert organometallic Pt based anticancer agents with a novel mechanism of action. Using a combination of in vitro and in vivo assays, we demonstrated that the development of a remarkably efficacious but kinetically inert Pt anticancer agent is feasible. Along with exerting promising antitumor efficacy in Pt-sensitive as well as Pt-resistant tumors in vivo, our best candidate has the ability to mitigate the nephrotoxicity issue associated with cisplatin. In addition to demonstrating, for the first time, the power of kinetic inertness in improving the therapeutic benefits of Pt based anticancer therapy, we describe the detailed mechanism of action of our best kinetically inert antitumor agent. This study will certainly pave the way for designing the next generation of anticancer drugs for effective treatment of various cancers.     

Energy-efficient syngas production through catalytic oxy-methane reforming reactions

The considerable recent interest in the conversion of stranded methane into transportable liquids as well as fuel cell technology has provided a renewed impetus to the development of efficient processes for the generation of syngas. The production of syngas (CO/H2), a very versatile intermediate, can be the most expensive step in the conversion of methane to value-added liquid fuels. The catalytic oxy reforming of methane, which is an energy-efficient process that can produce syngas at extremely high space-time yields, is discussed in this Review. As long-term catalyst performance is crucial for the wide-scale commercialization of this process, catalyst-related studies are abundant. Correspondingly, herein, emphasis is placed on discussing the different issues related to the development of catalysts for oxy reforming. Important aspects of related processes such as catalytic oxy-steam, oxy-CO2, and oxy-steam-CO2 processes will also be discussed.     

Total synthesis of clavosolide A

For the total synthesis of (−)-clavosolide A described herein, a Schmidt glycosidation reaction was used to attach the sugar moiety at an early stage in the synthesis to the 4-hydroxy group of the substituted tetrahydropyran unit of the molecule, which itself was built following a Ti(III)-mediated method developed by us earlier, and at the end, it was the Yamaguchi reaction that was successfully employed for the cyclodimerization of the two halves of the molecule leading to its total synthesis.