In vitro and in vivo production of new aminocoumarins by a combined biochemical, genetic, and synthetic approach

The aminocoumarin antibiotics clorobiocin, novobiocin, and coumermycin A(1) are inhibitors of bacterial gyrase. Their chemical structures contain amide bonds, formed between an aminocoumarin ring and an aromatic acyl component, which is 3-dimethylallyl-4-hydroxybenzoate in the case of novobiocin and clorobiocin. These amide bonds are formed under catalysis of the gene products of cloL, novL, and couL, respectively. We first examined the substrate specificity of the purified amide synthetases CloL, NovL, and CouL for the various analogs of the prenylated benzoate moiety. We then generated new aminocoumarin antibiotics by feeding synthetic analogs of the 3-dimethylallyl-4-hydroxybenzoate moiety to a mutant strain defective in the biosynthesis of the prenylated benzoate moiety. This resulted in the formation of 32 new aminocoumarin compounds. The structures of these compounds were elucidated using FAB-MS and (1)H-NMR spectroscopy.     

Tailoring of glycopeptide scaffolds by the acyltransferases from the teicoplanin and A-40,926 biosynthetic operons

The teicoplanin acyltransferase (Atf) responsible for N-acylation of the glucosamine moiety to create the teicoplanin lipoglycopeptide scaffold has recently been identified. Here we use that enzyme (tAtf) and the cognate acyltransferase from the related A-40,926 biosynthetic cluster (aAtf) to evaluate specificity for glycopeptide scaffolds and for the acyl-CoA donor. In addition to acylation of 2-aminoglucosyl glycopeptide scaffolds with k(cat) values of 400-2000 min(-1), both Atfs transfer acyl groups to regioisomeric 6-aminoglucosyl scaffolds and to glucosyl scaffolds at rates of 0.2-0.5 min(-1) to create variant lipoglycopeptides. Using the teicoplanin glycosyltransferase tGtfA, tAtf, and GtfD, a glycosyltransferase from the vancomycin producer, it is possible to assemble a novel lipoglycopeptide with GlcNAc at beta-OH-Tyr(6) and an N(6)-acyl-glucosaminyl-vancosamine at Phegly(4). This study illustrates the utility of chemo- and regioselective acyltransferases and glycosyltransferases to create novel lipoglycopeptides.     

Conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP during undecylprodigiosin and pyoluteorin biosynthesis

Several medically and agriculturally important natural products contain pyrrole moieties. Precursor labeling studies of some of these natural products have shown that L-proline can serve as the biosynthetic precursor for these moieties, including those found in coumermycin A(1), pyoluteorin, and one of the pyrroles of undecylprodigiosin. This suggests a novel mechanism for pyrrole biosynthesis. The biosynthetic gene clusters for these three natural products each encode proteins homologous to adenylation (A) and peptidyl carrier protein (PCP) domains of nonribosomal peptide synthetases in addition to novel acyl-CoA dehydrogenases. Here we show that the three proteins from the undecylprodigiosin and pyoluteorin biosynthetic pathways are sufficient for the conversion of L-proline to pyrrolyl-2-carboxyl-S-PCP. This establishes a novel mechanism for pyrrole biosynthesis and extends the hypothesis that organisms use A/PCP pairs to partition an amino acid into secondary metabolism.     

Synthesis of Spirocycles via Ni-Catalyzed Intramolecular Coupling of Thioesters and Olefins

A nickel-catalyzed intramolecular coupling of thioesters and olefins has been developed for the efficient synthesis of spirocycles, a privileged scaffold commonly found in natural products. This transformation is characterized by the simultaneous transfer of both acyl and thiol moieties to the alkene, with the suppression of decarbonylation and β-hydrogen elimination. Initial mechanistic investigations are consistent with an oxidative addition/olefin insertion/reductive elimination mechanism. The incorporated methylene sulfide substituent can undergo a variety of further reactions to increase molecular diversity and complexity. These results demonstrate that thioester derivatives can be used as powerful building blocks for the assembly of complex scaffolds.     

Hydrolysis of cyano(pyrrolyl-1)borates

The kinetics and mechanism of the hydrolysis of several cyano(pyrrolyl-1)borates in aqueous medium has been investigated. The hydrolysis of cyanophenyl(pyrrolyl-1)-borates, cyano(tripyrrolyl-1)borate and cyanohydro(pyrrolyl-1)borates proceeds via two kinds of reactions; (a) a special H⁺ ion catalyzed reaction (A-1 mechanism) and (b) a H⁺ ion concentration-independent process of S_N1 mechanism. In acidic medium the [BH₂(NC₄H₄)CN]⁻ anion is reversibly protonated at the -carbon of the pyrrolyl group and a product with composition C₄H₅N · BH₂CN, stable towards hydrolysis is also formed.

In the H⁺ ion catalyzed reaction the B---N bond very likely breaks, whereas upon the [H⁺] ion concentration-independent reaction a B---CN cleavage occurs. The presence of the cyano substituent significantly increases the hydrolytic stability of the B---N bond, whereas the pyrrolyl-1-substitution remarkably decreases the stability of the B---CN bonding.     

3D Plotted PCL Scaffolds for Stem Cell Based Bone Tissue Engineering

The ability to control the architecture and strength of a bone tissue engineering scaffold is critical to achieve a harmony between the scaffold and the host tissue. Rapid prototyping (RP) technique is applied to tissue engineering to satisfy this need and to create a scaffold directly from the scanned and digitized image of the defect site. Design and construction of complex structures with different shapes and sizes, at micro and macro scale, with fully interconnected pore structure and appropriate mechanical properties are possible by using RP techniques. In this study, RP was used for the production of poly(ε-caprolactone) (PCL) scaffolds. Scaffolds with four different architectures were produced by using different configurations of the fibers (basic, basic-offset, crossed and crossed-offset) within the architecture of the scaffold. The structure of the prepared scaffolds were examined by scanning electron microscopy (SEM), porosity and its distribution were analyzed by micro-computed tomography (µ-CT), stiffness and modulus values were determined by dynamic mechanical analysis (DMA). It was observed that the scaffolds had very ordered structures with mean porosities about 60%, and having storage modulus values about 1 × 10⁷ Pa. These structures were then seeded with rat bone marrow origin mesenchymal stem cells (MSCs) in order to investigate the effect of scaffold structure on the cell behavior; the proliferation and differentiation of the cells on the scaffolds were studied. It was observed that cell proliferation was higher on offset scaffolds (262000 vs 235000 for basic, 287000 vs 222000 for crossed structure) and stainings for actin filaments of the cells reveal successful attachment and spreading at the surfaces of the fibers. Alkaline phosphatase (ALP) activity results were higher for the samples with lower cell proliferation, as expected. Highest MSC differentiation was observed for crossed scaffolds indicating the influence of scaffold structure on cellular activities.     

A novel method for enzyme design

Rational design of enzymes is a stringent test of our understanding of protein structure and function relationship, which also has numerous potential applications. We present a novel method for enzyme design that can find good candidate protein scaffolds in a protein-ligand database based on vector matching of key residues. Residues in the vicinity of the active site were also compared according to a similarity score between the scaffold protein and the target enzyme. Suitable scaffold proteins were selected, and the side chains of residues around the active sites were rebuilt using a previously developed side-chain packing program. Triose phosphate isomerase (TIM) was used as a validation test for enzyme design. Selected scaffold proteins were found to accommodate the enzyme active sites and successfully form a good transition state complex. This method overcomes the limitations of the current enzyme design methods that use limited number of protein scaffold and based on the position of ligands. As there are a large number of protein scaffolds available in the Protein Data Band, this method should be widely applicable for various types of enzyme design.     

Scaffold diversity of exemplified medicinal chemistry space

The scaffold diversity of 7 representative commercial and proprietary compound libraries is explored for the first time using both Murcko frameworks and Scaffold Trees. We show that Level 1 of the Scaffold Tree is useful for the characterization of scaffold diversity in compound libraries and offers advantages over the use of Murcko frameworks. This analysis also demonstrates that the majority of compounds in the libraries we analyzed contain only a small number of well represented scaffolds and that a high percentage of singleton scaffolds represent the remaining compounds. We use Tree Maps to clearly visualize the scaffold space of representative compound libraries, for example, to display highly populated scaffolds and clusters of structurally similar scaffolds. This study further highlights the need for diversification of compound libraries used in hit discovery by focusing library enrichment on the synthesis of compounds with novel or underrepresented scaffolds.     

Free radical allyl transfers utilizing soluble non-cross-linked polystyrene and carbohydrate scaffold supports

Free radical allylations were studied using (1) soluble non-cross-linked polystyrene supports, (2) carbohydrate scaffolds, and (3) a combination of both synthetic motifs. Allylations on these custom designer supports provide easily purified products, free of tin residues. A D-xylose carbohydrate scaffold bearing a bromoester was used for a diastereoselective allyl tin transfer thermally at 80 degrees C and with Lewis acids. This is the first example of a diastereoselective radical reaction directed by a removable polymer-supported carbohydrate auxiliary.     

Multi-Material Scaffolds for Tissue Engineering

A trend in developing biocompatible scaffolds for tissue engineering has been to seek an ideal single material for which a given cell type will exhibit favorable behavior. While an ideal single material has proven elusive, scaffold manufacture using combinations of specialist materials can produce more versatile structures. By controlling the percentage and architecture of material components, mechanical properties, cell attachment, and proliferation may be optimized for a given function. Three specialist materials, poly-ϵ-caprolactone (PCL), fibrin, and alginate, were incorporated into multi-component scaffolds for a series of experiments testing each component with culture of fibroblasts. The rigid and formable PCL provided structure, the fibrin pore-filler allowed for cell attachment, and alginate thread provided a nutrient transfer pathway in lieu of a vascular system. The efficacy of these scaffolds was judged on fibroblast distribution and population after 7-12 days of culture.     

Coumarin formation in novobiocin biosynthesis: beta-hydroxylation of the aminoacyl enzyme tyrosyl-S-NovH by a cytochrome P450 NovI

BACKGROUND: Coumarin group antibiotics, such as novobiocin, coumermycin A1 and clorobiocin, are potent inhibitors of DNA gyrase. These antibiotics have been isolated from various Streptomyces species and all possess a 3-amino-4-hydroxy-coumarin moiety as their structural core. Prior labeling experiments on novobiocin established that the coumarin moiety was derived from L-tyrosine, probably via a beta-hydroxy-tyrosine (beta-OH-Tyr) intermediate. Recently the novobiocin gene cluster from Streptomyces spheroides was cloned and sequenced and allows analysis of the biosynthesis of the coumarin at the biochemical level using overexpressed and purified proteins. RESULTS: Two open reading frames (ORFs), NovH and NovI, from the novobiocin producer S. spheroides have been overexpressed in Escherichia coli, purified and characterized for tyrosine activation and oxygenation which are the initial steps in coumarin formation. The 65 kDa NovH has two predicted domains, an adenylation (A) and a peptidyl carrier protein (PCP), reminiscent of non-ribosomal peptide synthetases. Purified NovH catalyzes L-tyrosyl-AMP formation by its A domain, can be posttranslationally phosphopantetheinylated on the PCP domain, and accumulates the covalent L-tyrosyl-S-enzyme intermediate on the holo PCP domain. The second enzyme in the pathway, NovI, is a 45 kDa heme protein that functions as a cytochrome P450-type monooxygenase with specificity for the tyrosyl-S-NovH acyl enzyme. The product beta-OH-tyrosyl-S-NovH was detected by alkaline release and high performance liquid chromatography analysis of radioactive [3H]beta-OH-Tyr and by mass spectrometry. Also detected was 4-OH-benzaldehyde, a retro aldol breakdown product of beta-OH-Tyr. The amino acid released was (3R,2S)-3-OH-Tyr by comparison with authentic standards. CONCLUSIONS: This work establishes that NovH and NovI are responsible for the formation of a beta-OH-Tyr intermediate that is covalently tethered to NovH in novobiocin biosynthesis. Comparable A-PCP/P450 pairs for amino acid beta-hydroxylation are found in various biosynthetic gene clusters, such as ORF19/ORF20 in the chloroeremomycin cluster for tyrosine, CumC/CumD in the coumermycin A1 cluster for tyrosine, and NikP1/NikQ in the nikkomycin cluster for histidine. This phenomenon of covalent docking of the amino acid in a kinetically stable thioester linkage prior to chemical modification by downstream tailoring enzymes, could represent a common strategy for controlling the partitioning of the amino acid for incorporation into secondary metabolites.     

Synthesis and structures of homo- and heterobimetallic rhodium(I) and/or iridium(I) complexes of binucleating bis(1-pyrazolyl)methane ligands

The synthesis of a series of Rh(I) and Ir(I) homobimetallic complexes using three different linking scaffolds is described. The cyclooctadiene (COD) complexes [M(2)(COD)(2)(L(scaffold))][BAr(F)(4)](2) (2-7) where M = Rh(I) or Ir(I), and L(scaffold) = bis(1-pyrazolyl)methane ligands, p-C(6)H(4)[CH(pz)(2)](2) (1a), m-C(6)H(4)[CH(pz)(2)](2) (1b) and the anthracene-bridged 1,8-C(14)H(8)[CH(pz)(2)](2) (1c) were synthesized. The COD co-ligands of 2-7 were replaced with the carbonyl co-ligands to form the analogous homobimetallic complexes, [M(2)(CO)(4)(L(scaffold))][BAr(F)(4)](2) (8-13). The solid-state structures of the dicationic homobimetallic complexes 2, 3, 5, 6, 9, and 10, as well as cationic monometallic complexes 15 and 22 of ligands 1b and 1c respectively, were characterized using X-ray crystallography. The solid-state XRD structures of the resulting dirhodium and diiridium complexes with the para- and meta-phenylene and anthracene scaffolds show that there are distinct differences between structures of complexes 2-10 due to the variation in the scaffold structures, in particular the relative positions of the two metal centres. Heterobimetallic RhIr complexes of the m-C(6)H(4)[CH(pz)(2)](2) ligand were also synthesized using a stepwise approach, and the observed exchange of the metal centres in the heterobimetallic complexes was found to be dependent on the nature of the coligand.     

A Novel Series of 3,4‐Disubstituted Dihydropyrazoles: Synthesis and Evaluation for MAO Enzyme Inhibition

In this study, the authors have designed and synthesized a novel series of 3‐acyl‐4‐aryl‐4,5‐dihydropyrazoles, with the aim to obtain new potential scaffolds for the inhibition of both isoforms of monoamine oxidase (MAO) enzyme. The synthetic pathway to these compounds includes as a key step the 1,3‐dipolar cycloaddition reaction of diazomethane with a chalcone. All the compounds were fully characterized by means of spectroscopic and analytical data and showed specific inhibition against MAO A.     

Catalysis of Extracellular Deamination by a FAD‐Linked Oxidoreductase after Prodrug Maturation in the Biosynthesis of Saframycin A

The biosynthesis of antibiotics in bacteria is usually believed to be an intracellular process, at the end of which the matured compounds are exported outside the cells. The biosynthesis of saframycin A (SFM‐A), an antitumor antibiotic, requires a cryptic fatty acyl chain to guide the construction of a pentacyclic tetrahydroisoquinoline scaffold; however, the follow‐up deacylation and deamination steps remain unknown. Herein we demonstrate that SfmE, a membrane‐bound peptidase, hydrolyzes the fatty acyl chain to release the amino group; and SfmCy2, a secreted oxidoreductase covalently associated with FAD, subsequently performs an oxidative deamination extracellularly. These results not only fill in the missing steps of SFM‐A biosynthesis, but also reveal that a FAD‐binding oxidoreductase catalyzes an unexpected deamination reaction through an unconventional extracellular pathway in Streptmyces bacteria.     

Mining for bioactive scaffolds with scaffold networks: improved compound set enrichment from primary screening data

Identification of meaningful chemical patterns in the increasing amounts of high-throughput-generated bioactivity data available today is an increasingly important challenge for successful drug discovery. Herein, we present the scaffold network as a novel approach for mapping and navigation of chemical and biological space. A scaffold network represents the chemical space of a library of molecules consisting of all molecular scaffolds and smaller "parent" scaffolds generated therefrom by the pruning of rings, effectively leading to a network of common scaffold substructure relationships. This algorithm provides an extension of the scaffold tree algorithm that, instead of a network, generates a tree relationship between a heuristically rule-based selected subset of parent scaffolds. The approach was evaluated for the identification of statistically significantly active scaffolds from primary screening data for which the scaffold tree approach has already been shown to be successful. Because of the exhaustive enumeration of smaller scaffolds and the full enumeration of relationships between them, about twice as many statistically significantly active scaffolds were identified compared to the scaffold-tree-based approach. We suggest visualizing scaffold networks as islands of active scaffolds.     

In Vitro Evaluation of Combined Sulfated Silk Fibroin Scaffolds for Vascular Cell Growth

A combined sulfated silk fibroin scaffold is fabricated by modifying a knitted silk scaffold with sulfated silk fibroin sponges. In vitro hemocompatibility evaluation reveals that the combined sulfated silk fibroin scaffolds reduce platelet adhesion and activation, and prolong the activated partial thromboplastin time (APTT), thrombin time (TT), and prothrombin time (PT). The response of porcine endothelial cells (ECs) and smooth muscle cells (SMCs) on the scaffolds is studied to evaluate the cytocompatibility of the scaffolds. Vascular cells are seeded on the scaffolds and cultured for 2 weeks. The scaffolds demonstrate enhanced EC adhesion, proliferation, and maintenance of cellular functions. Moreover, the scaffolds inhibit SMC proliferation and induce expression of contractile SMC marker genes.

     

Protein assembly line components in prodigiosin biosynthesis: characterization of PigA,G,H,I,J

The red streptomycete metabolite prodigiosin has a unique tripyrrolic structure with two of the three pyrrolyl moieties in tandem. Five enzymes, PigA,G,H,I, and J, are involved in dipyrrole (rings A and B) formation. We have heterologously expressed and purified from Escherichia coli these five enzymes. At first, pyrrole ring A is formed on the peptidyl carrier protein PigG by one of two possible ways: (i) by action of the adenylation domain PigI that transforms l-proline into l-prolyl-AMP and by the flavoprotein dehydrogenase PigA responsible for the four-electron oxidation reaction; (ii) by loading with the pyrrolyl-2-carboxyl-(S)-pantetheinyl moiety from synthetic pyrrolyl-CoA using the phosphopantetheinyl transferase Sfp. Subsequently, pyrrole ring B is constructed by PigH after the transfer of ring A to the ketosynthase of PigJ. PigH consists of three domains: two acyl carrier proteins (ACPs) and a seryltransferase (SerT). Using HPLC and nanospray-Fourier Transform Mass Spectrometry (nFTMS), we established that all three domains of PigH undergo post-translational modifications and gained insight into the machinery involved in 2,2-dipyrrole biosynthesis.     

A one-pot preparation of N-2-mercaptobenzoyl-amino amides

The HIV-1 nucleocapsid (NCp7), structurally defined by zinc-binding domains, participates in crucial stages of the HIV-1 lifecycle and is mutationally nonpermissive, making it an attractive anti-HIV target. Mode of action studies have shown that the secondary structure and activity of NCp7 can be disrupted by acyl transfer from N-2-mercaptobenzoyl-amino amides. We have developed an improved one-pot reaction that affords N-2-mercaptobenzoyl-amino acids on multi-gram scales. This synthetic route allows for rapid modular construction and has greatly expanded the scope of easily accessible potential NCp7 inhibitors.     

Catalysis of Extracellular Deamination by a FAD-Linked Oxidoreductase after Prodrug Maturation in the Biosynthesis of Saframycin A

The biosynthesis of antibiotics in bacteria is usually believed to be an intracellular process, at the end of which the matured compounds are exported outside the cells. The biosynthesis of saframycin A (SFM-A), an antitumor antibiotic, requires a cryptic fatty acyl chain to guide the construction of a pentacyclic tetrahydroisoquinoline scaffold; however, the follow-up deacylation and deamination steps remain unknown. Herein we demonstrate that SfmE, a membrane-bound peptidase, hydrolyzes the fatty acyl chain to release the amino group; and SfmCy2, a secreted oxidoreductase covalently associated with FAD, subsequently performs an oxidative deamination extracellularly. These results not only fill in the missing steps of SFM-A biosynthesis, but also reveal that a FAD-binding oxidoreductase catalyzes an unexpected deamination reaction through an unconventional extracellular pathway in Streptmyces bacteria.