Synthesis and derivatization of daptomycin: a chemoenzymatic route to acidic lipopeptide antibiotics

Daptomycin is a branched cyclic nonribosomally assembled acidic lipopeptide, which is the first clinically approved antibiotic of this class. Here we show that the recombinant cyclization domain of the Streptomyces coelicolor calcium-dependent antibiotic (CDA) nonribosomal peptide synthetase (NRPS) is a versatile tool for the chemoenzymatic generation of daptomycin derivatives. Linear CDA undecapeptide thioesters with single exchanges at six daptomycin-specific residues were successfully cyclized by CDA cyclase. Simultaneous incorporation of all six of these residues into the peptide backbone and elongation of the N-terminus of CDA by two residues yielded a daptomycin derivative that lacked only the beta-methyl group of l-3-methylglutamate. Bioactivity studies with several substrate analogues revealed a significant role of nonproteinogenic constituents for antibacterial potency. In accordance with acidic lipopeptides, the bioactivity of the chemoenzymatic assembled daptomycin analogue is dependent on the concentration of calcium ions. Single deletions of the four acidic residues in the peptide backbone suggest that only two aspartic acid residues are essential for antimicrobial potency. These two residues are strictly conserved among other nonribosomal acidic lipopeptides and the EF-motif of ribosomally assembled calmodulin. Based on these findings CDA cyclase is a versatile catalyst that can be used to generate novel daptomycin derivatives that are otherwise difficult to obtain by chemical modification of the parental tridecapeptide to improve further its therapeutic activity.     

Absolute Rate Constants for the Addition of the 1‐(tert‐Butoxy)carbonylethyl Radical onto Cyclic Alkenes in Solution

Absolute rate constants are reported for the addition of the 1‐[(tert‐butoxy)carbonyl]ethyl (= 2‐(1,1‐dimethylethoxy)‐1‐methyl‐2‐oxoethyl) radical ^.CHMeCO₂(t‐Bu) to several cyclic and monosubstituted alkenes in MeCN as obtained by time‐resolved electron paramagnetic resonance (EPR). The activation energies for the addition of this alkyl radical are mainly governed by the addition enthalpy but are also substantially lowered by the ambiphilic effect and by relief of cyclic strain.     

Synthesis of homochiral 2-C-perfluoroalkyl substituted d- and l-riboses

Homochiral 2-C-perfluoroalkyl substituted d- and l-riboses were synthesized via Barbier, Grignard and Ruppert type reactions. The influence of the size of the perfluoroalkyl groups, attached to C-2, on the furanose/pyranose as well as on the α-furanose/β-furanose and α-pyranose/β-pyranose ratio in solution was studied.     

Butadienyloxiran-Dihydrooxepin-Isomerisierung. Ringerweiterungsreaktionen von sterisch fixierten und benzoanellierten Epoxyhexadienen durch 1,7-Elektrocyclisierung konjugierter Carbonyl-Ylide

Butadienyloxirane-Dihydrooxepine Isomerisation. Ring Expansion Reactions of Sterically Fixed and Benzoannelated Epoxyhexadienes by 1,7-Electrocyclisation of Conjugated Carbonyl Ylides Thermal ring cleavage of specifically substituted oxiranes results in the formation of conjugated carbonyl ylide intermediates which react by 1,5- and/or 1,7-electrocyclisation to give ring-expanded products. While the spirooxiranes 5t, 6t , and 12t are transformed, as expected, only into 2,3-dihydrofurans ( 21, 22, 50 ), the geometrically fixed compounds give rise to the formation of seven-membered ring isomers either partially ( 6c ), or predominantly ( 5c ), or exclusively ( 7 – 11, 12c ). 1,7-Dipolar cyclisations also take place with participation of one or even two aromatic double bonds ( 7 → 52, 8 → 53, 9 → 54, 12c → 57 , and 10 → 55, 11 → 56 , resp.) affording mono- and dibenzo-dihydrooxepines, respectively. The rearrangements of 5c to 27 and 6c to 28 show for the first time that the 8π-ring closure of 2-oxaheptatrienyl dipoles proceeds in the theoretically predicted conrotatory manner. The exclusive, i.e. periselective formation of dihydrooxepines during the thermolysis of compounds 7 – 11, 12c is explained by assuming a helical geometry of the dipolar intermediates in which the stereoelectronic situation is specially suitable for the – entropically less advantageous – 1,7-cyclisation process.     

An alternative sampling algorithm for use in liquid chromatography/tandem mass spectrometry experiments

In liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses of complex peptide mixtures, dynamic exclusion functions are used to minimize repeat selections of identical precursors for collision induced dissociation (CID). We describe a new algorithm for the dynamic exclusion of m/z values during LC/MS/MS. Full-scan based peak exclusion (Fulspec) uses a simplified model of chromatographic peak formation to detect and exclude contaminants present throughout the run or that lead to broad peaks. Therefore, instead of excluding peptides from fragment analysis according to a rigidly predefined time window, the chromatographic properties of the detected analytes are used. The algorithm was tested on two datasets derived from previously published experiments. Fulspec achieves a distribution of CID spectra with minimal tailing on the retention time axis, without resorting to rigid exclusion of m/z values. The procedure further excludes intensities with a bias towards low-quality CID spectra. This combination frees up valuable analytical capacity. The underlying intensity vs. quality analyses challenge the assumption that abundant precursors automatically give the best identifications. Further validation of the algorithm will require its incorporation by equipment manufacturers into the instrument control programs.     

Cis‐trans Isomerism in Copper(II) Complexes with N‐acyl Thiourea Ligands

The N‐acyl thiourea complexes bis[N,N‐diethyl‐N′‐(p‐nitrobenzoyl)‐thioureato]copper(II) ( 1a,1b ) and bis(N,N‐diphenyl‐N′‐benzoylthioureato)copper(II) ( 2a,2b ) crystallize in each case in two modifications. X‐ray structural analysis shows that 1a and 1b are cis‐trans isomers. This is very unusual for N‐acyl thioureato complexes because with exception of one platinum(II) complex up to now only cis complexes have been found. In contrast X‐ray structural analysis of both forms 2a and 2b of the other complex shows no cis‐trans pair. Both modifications are cis complexes. In solution both isomers of the copper(II) complexes are observable by EPR spectroscopy.     

Ringerweiterungsreaktionen von (Z)-styryloxiranen unter Phenylring-Beteiligung: bildung von 2,7-dihydro-3,4-benzoxepinen

The thermal ring expansion reaction of (Z)-styryloxiranes ($\text{7}$-$\text{9}$) involves phenylring participation leading to 2,7-dihydro-3,4-benzoxepins ($\text{10}$-$\text{12}$).     

Quecksilber(II)‐chlorid‐ und ‐iodid‐Komplexe von Dithia‐ und Tetrathiakronenethern

Mercury(II) Chloride and Iodide Complexes of Dithia‐ and Tetrathiacrown Ethers The complexes [(HgCl₂)₂((ch)₂30S₄O₆)] ( 1 ), [HgCl₂(mn21S₂O₅)] ( 2 ), [HgCl₂(ch18S₂O₄)] ( 3 ) and [HgI(meb12S₂O₂)]₂[Hg₂I₆] ( 4 ) have been synthesized, characterized and their crystal structures were determined. In [(HgCl₂)₂((ch)₂30S₄O₆)] two HgCl₂ units are discretely bonded within the ligand cavity of the 30‐membered dichinoxaline‐tetrathia‐30‐crown‐10 ((ch)₂30S₄O₆) forming a binuclear complex. HgCl₂ forms 1 : 1 “in‐cavity” complexes with the 21‐membered maleonitrile‐dithia‐21‐crown‐7 (mn21S₂O₅) ligand and the 18‐membered chinoxaline‐dithia‐18‐crown‐6 (ch18S₂O₄) ligand, respectively. The 12‐membered 4‐methyl‐benzo‐dithia‐12‐crown‐4 (meb12S₂O₂) ligand gave with two equivalents HgI₂ the compound [HgI(meb12S₂O₂)]₂[Hg₂I₆]. In the cation [HgI(meb12S₂O₂)]⁺ meb12S₂O₂ forms with the cation HgI⁺ a half‐sandwich complex.     

Ion-pair reversed-phase high-performance liquid chromatography analysis of oligonucleotides: retention prediction

An ion-pair reversed-phase HPLC method was evaluated for the separation of synthetic oligonucleotides. Mass transfer in the stationary phase was found to be a major factor contributing to peak broadening on porous C18 stationary phases. A small sorbent particle size (2.5 microm), elevated temperature and a relatively slow flow-rate were utilized to enhance mass transfer. A short 50 mm column allows for an efficient separation up to 30mer oligonucleotides. The separation strategy consists of a shallow linear gradient of organic modifier, optimal initial gradient strength, and the use of an ion-pairing buffer. The triethylammonium acetate ion-pairing mobile phases have been traditionally used for oligonucleotide separations with good result. However, the oligonucleotide retention is affected by its nucleotide composition. We developed a mathematical model for the prediction of oligonucleotide retention from sequence and length. We used the model successfully to select the optimal initial gradient strength for fast HPLC purification of synthetic oligonucleotides. We also utilized ion-pairing mobile phases comprised of triethylamine (TEA) buffered by hexafluoroisopropanol (HFIP). The TEA-HFIP aqueous buffers are useful for a highly efficient and less sequence-dependent separation of heterooligonucleotides.