Studies on the solution- and solid-state structure of patellin 2

Catalysts for the Enzymatic Lipidation of Peptides

Biologically active peptides are a major growing class of drugs, but their therapeutic potential is constrained by several limitations including bioavailability and poor pharmacokinetics. The attachment of functional groups like lipids has proven to be a robust and effective strategy for improving their therapeutic potential. Biochemical and bioactivity-guided screening efforts have identified the cyanobactins as a large class of ribosomally synthesized and post-translationally modified peptides (RiPPs) that are modified with lipids. These lipids are attached by the F superfamily of peptide prenyltransferase enzymes that utilize 5-carbon (prenylation) or 10-carbon (geranylation) donors. The chemical structures of various cyanobactins initially showed isoprenoid attachments on Ser, Thr, or Tyr. Biochemical characterization of the F prenyltransferases from the corresponding clusters shows that the different enzymes have different acceptor residue specificities but are otherwise remarkably sequence tolerant. Hence, these enzymes are well suited for biotechnological applications. The crystal structure of the Tyr O-prenyltransferase PagF reveals that the F enzyme shares a domain architecture reminiscent of a canonical ABBA prenyltransferase fold but lacks secondary structural elements necessary to form an enclosed active site. Binding of either cyclic or linear peptides is sufficient to close the active site to allow for productive catalysis, explaining why these enzymes cannot use isolated amino acids as substrates.Almost all characterized isoprenylated cyanobactins are modified with 5-carbon isoprenoids. However, chemical characterization demonstrates that the piricyclamides are modified with a 10-carbon geranyl moiety, and in vitro reconstitution of the corresponding PirF shows that the enzyme is a geranyltransferase. Structural analysis of PirF shows an active site nearly identical with that of the PagF prenyltransferase but with a single amino acid substitution. Of note, mutation at this residue in PagF or PirF can completely switch the isoprenoid donor specificity of these enzymes. Recent efforts have resulted in significant expansion of the F family with enzymes identified that can carry out C-prenylations of Trp, N-prenylations of Trp, and bis-N-prenylations of Arg. Additional genome-guided efforts based on the sequence of F enzymes identify linear cyanobactins that are α-N-prenylated and α-C-methylated by a bifunctional prenyltransferase/methyltransferase fusion and a bis-α-N- and α-C-prenylated linear peptide. The discovery of these different classes of prenyltransferases with diverse acceptor residue specificities expands the biosynthetic toolkit for enzymatic prenylation of peptide substrates.In this Account, we review the current knowledge scope of the F family of peptide prenyltransferases, focusing on the biochemical, structure-function, and chemical characterization studies that have been carried out in our laboratories. These enzymes are easily amenable for diversity-oriented synthetic efforts as they can accommodate substrate peptides of diverse sequences and are thus attractive catalysts for use in synthetic biology approaches to generate high-value peptidic therapeutics.

Regio- and stereoselective synthesis of thiazoline derivatives via the thioketene-induced ring expansion of aziridines

Metal-free thioketene-induced ring expansion of aziridines gave 4-alkylthiazolines stereospecifically from 2-alkylaziridines through an intramolecular substitution at the less substituted ring carbon and 5-arylthiazolines stereoselectively from 2-arylaziridines via tandem ring cleavage and formation through intimate ion-pair intermediates after nucleophilic addition of aziridines to thioketenes generated from 4-substituted 1,2,3-thiadiazoles in the presence of a base.

The Biochemistry and Structural Biology of Cyanobactin Pathways: Enabling Combinatorial Biosynthesis

Cyanobactin biosynthetic enzymes have exceptional versatility in the synthesis of natural and unnatural products. Cyanobactins are ribosomally synthesized and posttranslationally modified peptides synthesized by multistep pathways involving a broad suite of enzymes, including heterocyclases/cyclodehydratases, macrocyclases, proteases, prenyltransferases, methyltransferases, and others. Here, we describe the enzymology and structural biology of cyanobactin biosynthetic enzymes, aiming at the twin goals of understanding biochemical mechanisms and biosynthetic plasticity. We highlight how this common suite of enzymes may be utilized to generate a large array or structurally and chemically diverse compounds.

YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function

With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.

Crystal structures of ethyl {2-[4-(4-iso-propyl-phen-yl)thia-zol-2-yl]phen-yl}carbamate and ethyl {2-[4-(3-nitro-phen-yl)thia-zol-2-yl]phen-yl}carbamate

The title compounds, C21H22N2O2S (I) and C18H15N3O4S (II), are structural analogs of the alkaloid Thio-sporine B. Both mol-ecules adopt a near-planar V-shaped conformation, which is consolidated by intra-molecular N-H⋯N and C-H⋯O hydrogen bonds. The crystal structure of (I) consists of mlecular stacks along the a axis, in which the mol-ecules are linked to each other by π(S)⋯π(C) inter-actions. In the crystal of (II), mol-ecules are linked into chains by C-H⋯O hydrogen bonds and the chains are cross-linked into (100) sheets by π-π stacking inter-actions.

Metabolic model for diversity-generating biosynthesis

A conventional metabolic pathway leads to a specific product. In stark contrast, there are diversity-generating metabolic pathways that naturally produce different chemicals, sometimes of great diversity. We demonstrate that for one such pathway, tru, each ensuing metabolic step is slower, in parallel with the increasing potential chemical divergence generated as the pathway proceeds. Intermediates are long lived and accumulate progressively, in contrast with conventional metabolic pathways, in which the first step is rate-limiting and metabolic intermediates are short-lived. Understanding these fundamental differences enables several different practical applications, such as combinatorial biosynthesis, some of which we demonstrate here. We propose that these principles may provide a unifying framework underlying diversity-generating metabolism in many different biosynthetic pathways.

Cyanobactins from Cyanobacteria: Current Genetic and Chemical State of Knowledge

Cyanobacteria are considered to be one of the most promising sources of new, natural products. Apart from non-ribosomal peptides and polyketides, ribosomally synthesized and post-translationally modified peptides (RiPPs) are one of the leading groups of bioactive compounds produced by cyanobacteria. Among these, cyanobactins have sparked attention due to their interesting bioactivities and for their potential to be prospective candidates in the development of drugs. It is assumed that the primary source of cyanobactins is cyanobacteria, although these compounds have also been isolated from marine animals such as ascidians, sponges and mollusks. The aim of this review is to update the current knowledge of cyanobactins, recognized as being produced by cyanobacteria, and to emphasize their genetic clusters and chemical structures as well as their bioactivities, ecological roles and biotechnological potential.

Assessing the combinatorial potential of the RiPP cyanobactin tru pathway

Ribosomally produced natural products, the RiPPs, exhibit features that are potentially useful in the creation of large chemical libraries using simple mutagenesis. RiPPs are encoded on ribosomal precursor peptides, but they are extensively posttranslationally modified, endowing them with properties that are useful in drug discovery and biotechnology. In order to determine which mutations are acceptable, strategies are required to determine sequence selectivity independently of the context of flanking amino acids. Here, we examined the absolute sequence selectivity of the trunkamide cyanobactin pathway, tru. A series of random double and quadruple simultaneous mutants were synthesized and produced in Escherichia coli. Out of a total of 763 mutated amino acids examined in 325 unique sequences, 323 amino acids were successfully incorporated in 159 sequences, leading to >300 new compounds. Rules for tru sequence selectivity were determined, which will be useful for the design and synthesis of combinatorial biosynthetic libraries. The results are also interpreted in comparison to the known natural products of tru and pat cyanobactin pathways.

Thiazoline peptides and a tris-phenethyl urea from Didemnum molle with anti-HIV activity

As part of our screening for anti-HIV agents from marine invertebrates, the MeOH extract of Didemnum molle was tested and showed moderate in vitro anti-HIV activity. Bioassay-guided fractionation of a large-scale extract allowed the identification of two new cyclopeptides, mollamides E and F (1 and 2), and one new tris-phenethyl urea, molleurea A (3). The absolute configurations were established using the advanced Marfey's method. The three compounds were evaluated for anti-HIV activity in both an HIV integrase inhibition assay and a cytoprotective cell-based assay. Compound 2 was active in both assays with IC(50) values of 39 and 78 μM, respectively. Compound 3 was active only in the cytoprotective cell-based assay, with an IC(50) value of 60 μM.

Ribosomal route to small-molecule diversity

The cyanobactin ribosomal peptide (RP) natural product pathway was manipulated to incorporate multiple tandem mutations and non-proteinogenic amino acids, using eight heterologous components simultaneously expressed in Escherichia coli . These studies reveal the potential of RPs for the rational synthesis of complex, new small molecules over multiple-step biosynthetic pathways using simple genetic engineering.

Thiazole and oxazole alkaloids: isolation and synthesis

Thiazoles, oxazole and their corresponding reduced derivatives, thiazolines and oxazolines, are found in marine sources exhibiting significant biological activities. The isolation, synthetic, and biological studies of these natural products, covering literature from January 2007 to June 2010, are summarized.

Cyanobactins-ribosomal cyclic peptides produced by cyanobacteria

Cyanobactins are small cyclic peptides that are produced by a diverse selection of cyanobacteria living in symbioses as well as terrestrial, marine, or freshwater environments. They include compounds with antimalarial, antitumor, and multidrug reversing activities and potential as pharmaceutical leads. Cyanobactins are produced through the proteolytic cleavage and cyclization of precursor peptides coupled with further posttranslational modifications such as heterocyclization, oxidation, or prenylation of amino acids. Cyanobactin gene clusters encode two proteases which cleave and cyclisize the precursor peptide as well as proteins participating in posttranslational modifications. The bioinformatic mining of cyanobacterial genomes has led to the discovery of novel cyanobactins. Heterologous expression of these gene clusters provided insights into the role of the genes participating in the biosynthesis of cyanobactins and facilitated the rational design of novel peptides. Enzymes participating in the biosynthesis of cyanobactins may prove useful as catalysts for producing novel cyclic peptides in the future. The recent discovery of the cyanobactin biosynthetic pathway in cyanobacteria extends our knowledge of their potential as producers of interesting metabolites.

A global assembly line for cyanobactins

More than 100 cyclic peptides harboring heterocyclized residues are known from marine ascidians, sponges and different genera of cyanobacteria. Here, we report an assembly line responsible for the biosynthesis of these diverse peptides, now called cyanobactins, both in symbiotic and free-living cyanobacteria. By comparing five new cyanobactin biosynthetic clusters, we produced the prenylated antitumor preclinical candidate trunkamide in Escherichia coli culture using genetic engineering.

Solid-state nuclear magnetic resonance spectroscopy--pharmaceutical applications

Solid-state nuclear magnetic resonance (NMR) spectroscopy has become an integral technique in the field of pharmaceutical sciences. This review focuses on the use of solid-state NMR techniques for the characterization of pharmaceutical solids (drug substance and dosage form). These techniques include methods for (1) studying structure and conformation, (2) analyzing molecular motions (relaxation and exchange spectroscopy), (3) assigning resonances (spectral editing and two-dimensional correlation spectroscopy), and (4) measuring internuclear distances.

Solution structure of the antitumor candidate trunkamide A by 2D NMR and restrained simulated annealing methods

Trunkamide A (1) is a cyclic heptapeptide extracted from the ascidian Lissoclinum sp. and has shown very promising cytotoxic activity. This compound incorporates several of the motifs commonly observed in the Patellin family, including dimethylallyl (Dma) Thr and Ser side chains and a thiazoline heterocycle. Given that little is known about the structures adopted by the cyclopeptides of the Patellin family, and with the aim of establishing structure-activity relationships, we have carried out the conformational analysis of trunkamide A by a combination of 2D NMR experiments and simulated annealing calculations. Our results show that the conformation of 1 is very rigid and is dominated by the volume of the dimethylallyl side chains and two trans-annular hydrogen bonds. We have also studied the conformation of 2, the l-Phe diastereoisomer of 1, the analysis of which provides a possible rationale for its epimerization to 1, a process that is observed in solution. Finally, we show how a thorough NMR characterization can be used, in combination with simulated annealing methods, to confirm the configuration of a stereogenic center in the backbone of a rigid cyclic peptide such as trunkamide A (1).

Total synthesis and revision of stereochemistry of the marine metabolite trunkamide A

The isolation of the cytotoxic Lissoclinum sp. metabolite trunkamide A was reported in 1996. After completion of a total synthesis in 1999, it became clear that the structure of this marine natural product had to be revised. We now report the first preparation of actual trunkamide A in a total synthesis that serves as an unambiguous structural and stereochemical proof. Highlights of our synthetic strategy are a Lewis acid assisted aziridine opening that was used for the preparation of the novel reverse-prenylated serine and threonine side chains as well as an efficient oxazoline-thiazoline interconversion on the macrocyclic skeleton. In addition, several stereoisomers prepared by complementary synthetic protocols serve to illustrate the general scope of our methodology and confirm the configurational assignment.

New cyclic peptides from the ascidian Lissoclinum patella

Four new cyclic peptides, patellamide G (2) and ulithiacyclamides E-G (3-5), along with the known patellamides A-C (6-8) and ulithiacyclamide B (9), were isolated from the ascidian Lissoclinum patella collected in Pohnpei, Federated States of Micronesia. The planar structures of these peptides were determined from 1D and 2D 1H and 13C NMR spectra. The absolute stereochemistries of the amino acid units, except for cysteine, were assigned by chiral GC analysis of N(O)-trifluoroacetyl isopropyl ester derivatives of amino acids obtained by acid hydrolysis of the intact and ozonized peptides. The structures of ulithiacyclamides E-G (3-5) were confirmed by chemical conversion. Patellamides B (7) and C (8) exhibited in vitro modulation of multidrug resistance in CEM/VBL100 cells.

Isolation and structure of the human cancer cell growth inhibitory cyclodepsipeptide dolastatin 16

An investigation of the sea hare Dolabella auricularia from Papua New Guinea has led to discovery of the new cyclodepsipeptide dolastatin 16 (3) containing two new amino acid units designated dolamethylleuine (Dml) and dolaphenvaline (Dpv). The structural elucidation was achieved by means of high-field (500 MHz) NMR and tandem MS/MS mass spectral interpretations and allowed the assignment of cyclo-(Pro-Dpv-Pro-Dml-O-Lac-Pro-O-Hiv-MeVal). The new depsipeptide exhibited strong inhibition of growth against a variety of human cancer cell lines.

The Kapakahines, Cyclic Peptides from the Marine Sponge Cribrochalina olemda

Four cyclic peptides, kapakahines A-D, were isolated from the marine sponge Cribrochalina olemda. Their structures including complete stereochemistry were elucidated by spectral analysis and chemical degradation. The unique structural feature of these peptides is the lack of an amide linkage between two tryptophan residues. Instead the ring is closed by a bond from the indole nitrogen of Trp-1 to the beta-carbon of Trp-2.

Molecular conformation of ascidiacyclamide, a cytotoxic cyclic peptide from Ascidian: X-ray analyses of its free form and solvate crystals

In order to investigate the conformational variation of ascidiacyclamide, a cytotoxic cyclic peptide from marine tunicate Ascidian, single crystals were prepared from ethanol and aqueous ethanol solutions as its free form (crystal I) and H2O/0.5 C2H5OH solvate (crystal II), respectively, and were determined by the x-ray diffraction method. Crystal I showed a pseudo C2-symmetric saddle-shaped rectangular conformation. Similar conformations were also observed in crystal II, where there were two crystallographically independent C2-symmetric molecules (named Mol-A and -B) per asymmetric unit. Mol-A and -B included H2O and H2O/C2H5OH solvents within their ring structures, respectively. These water and ethanol molecules were located on the crystallographic dyad axes, and were stabilized by the van der Waals contacts (including hydrogen bonds) with the polar-ring N atoms and nonpolar D-Val side-chain atoms. The conformational characteristics of ascidiacyclamide and its fluctuation/variation were discussed based on the present and previously reported x-ray results.