Exploration of the molecular origin of the azinomycin epoxide: timing of the biosynthesis revealed

Streptomyces sahachiroi whole cell feeding experiments, utilizing putative precursors labeled with stable isotopes, established that the epoxide unit of the DNA cross-linked agents, azinomycin A and B, proceeds via a valine-dependent pathway and that hydroxylation and dehydration precedes formation of the terminal epoxide. Sodium 3-methyl-2-oxobutenoate, formed through a transimination reaction, was shown to be the penultimate precursor incorporated into the azinomycin epoxide.     

In vitro biosynthesis of the antitumor agent azinomycin B

[reaction: see text] Azinomycins have potential therapeutic value as antitumor agents; however, their biosynthesis is poorly understood. Here, we provide the first demonstration of a protein cell-free system capable of supporting complete in vitro biosynthesis of the antitumor agent azinomycin B. The cell-free system is utilized to probe the cofactor dependence and substrate requirements of the pathway en route to azinomycin.     

Molecular modeling of DNA cross-linking analogues based on the azinomycin scaffold

In this work, we present molecular modeling studies carried out using six DNA sequences and six azinomycin analogues, including the naturally occurring compound azinomycin B, selected on the basis of known cell cytotoxicity and structural analogies (epoxide and aziridine alkylating moieties). Among several computational methods the Stochastic Dynamics with Energy Minimization (SDEM) approach yielded results superior to the others with the natural compound (r(2) > 0.9) and was adopted for studying other DNA adducts, obtaining good correlation between the average theoretical cross-linking properties and the antitumor activity scale. As a result, some interesting SAR considerations have been highlighted and a cross-linking conformation different from that of the azinomycin was identified in a less potent, simplified analogue.     

Dependence of DNA sequence selectivity and cell cytotoxicity on azinomycin A and B epoxyamide stereochemistry

Evaluation of the importance of C18/C19 stereochemistry of azinomycin A/B epoxyamide partial structures with respect to DNA alkylation sequence selectivity is reported using a unique assay with a DNA oligomer containing imbedded normal (5'-GGC-3'/3'-CCG-5') and inverted (5'-CGG-3'/3'-GCC-5') azinomycin consensus cross-linking sequences. Both species were found to have unique selectivity profiles and alkylate DNA in a manner distinct from azinomycin B. Computational docking experiments support altered binding modes for the enantiomers.     

Studies on the mechanism of action of azinomycin B: definition of regioselectivity and sequence selectivity of DNA cross-link formation and clarification of the role of the naphthoate

Evaluation of the sequence selectivity, noncovalent association, and orientation of the DNA cross-linking agent azinomycin B on its duplex DNA receptor is described. A strong correlation between sequence nucleophilicity and cross-linking yield was observed, and steric effects due to the thymine C5-methyl group were identified. Detailed studies on the role of the azinomycin naphthoate using viscometry, fluorescence contact energy transfer, and DNA unwinding assays point to a nonintercalative binding mode for this group. A kinetic assay for agent regioselectivity was used to determine the orientation of binding and covalent cross-link formation.     

The first biosynthetic studies of the azinomycins: acetate incorporation into azinomycin B

13C-labelled acetate efficiently labels the antitumour natural product azinomycin B, revealing a polyketide origin for the naphthoate fragment, that threonine is the probable precursor of the enol fragment, and that alpha-ketoglutarate is a probable precursor of the aziridine fragment.     

Characterization of the azinomycin B biosynthetic gene cluster revealing a different iterative type I polyketide synthase for naphthoate biosynthesis

Azinomycin B is a complex natural product containing densely assembled functionalities with potent antitumor activity. Cloning and sequence analysis of the azi gene cluster revealed an iterative type I polyketide synthase (PKS) gene, five nonribosomal peptide synthetases (NRPSs) genes and numerous genes encoding the biosynthesis of unusual building blocks and tailoring steps for azinomycin B production. Characterization of AziB as a 5-methyl-naphthoic acid (NPA) synthase showed a distinct selective reduction pattern in aromatic polyketide biosynthesis governed by bacterial iterative type I PKSs. Heterologous expression established the PKS-post modification route from 5-methyl-NPA to reach the first building block 3-methoxy-5-methyl-NPA. This proposed azinomycin B biosynthetic pathway sets the stage to investigate the enzymatic mechanisms for building structurally unique and pharmaceutically important groups, including the unprecedented azabicyclic ring system and highly active epoxide moiety.     

Delineating noncovalent interactions between the azinomycins and double-stranded DNA: importance of the naphthalene substitution pattern on interstrand cross-linking efficiency

[reaction: see text] Using a series of synthetic azinomycin analogues, it is shown that the efficiency of in vitro DNA interstrand cross-linking is markedly reduced when either the C-5' methyl group or both the C-5' methyl and C-3' methoxy groups are deleted from the naphthalene ring.     

Synthesis of functional "top-half" partial structures of azinomycin a and B

The design and synthesis of a detailed series of functional "top-half" substructures of azinomycin A and B is described.     

Role of the azinomycin naphthoate and central amide in sequence-dependent DNA alkylation and cytotoxicity of epoxide-bearing substructures

Studies report a strong correlation between duplex DNA alkylation and in vitro cytotoxicity for a series of azinomycin partial structures 2-6 bearing the biologically relevant epoxide. Compounds lacking the naphthoate ester (e.g., 5 and 6) were poorly reactive toward DNA and were biologically inactive, as were compounds bearing the naphthoate but lacking the terminal carboxamide (e.g., 2). Compounds were evaluated for cytotoxicity against two breast cancer cell lines. [structure: see text]     

Synthesis of 1-azabicyclo[3.1.0]hexane systems

The synthesis of aziridino[1,2-a]pyrrolidine systems related to the azinomycin family of antitumor agents is reported and was based on an intramolecular addition-elimination reaction sequence. Department of Chemistry, Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA. Published in Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1632–1635, December, 1998.     

Concise route to α-acylamino-β-keto amides: application to the synthesis of a simplified azinomycin A analogue

Condensation of acid chlorides (alkyl, aryl or heteroaryl) with N,N′-dialkyl α-acylamino malonamides in the presence of magnesium ethoxide provides a direct route to α-acylamino-β-keto amides in moderate to good yields (46–95%). Using this method, a concise route to an enantiomerically enriched 1-azabicyclo[3.1.0]hexane containing most of the elements of the ‘right-hand’ domain of azinomycin A has been developed.     

Design and synthesis of a DNA-crosslinking azinomycin analogue

The azinomycins are potent antitumour antibiotics that are able to crosslink DNA, but are relatively unstable and unlikely to progress as therapeutic candidates. A prototype analogue 4 with more clinical potential has been designed and synthesised and incorporates the epoxide function of the azinomycins and a nitrogen mustard. Two further analogues 5 and 6 that can alkylate DNA but cannot crosslink the duplex have also been synthesised. Compound 4 crosslinks DNA efficiently at nM concentrations. Compounds 4-6 were submitted to the NCI 60 cell line screen and have similar antitumour activity, although 4 is slightly less active than the non-crosslinking compounds. These observations will be important in the design of further azinomycin analogues with antitumour activity.     

Mode of action and biosynthesis of the azabicycle-containing natural products azinomycin and ficellomycin

Only a handful of aziridine-containing natural products have been identified out of the more than 100,000 natural products characterized to date. Among this class of compounds, only the azinomycins (azinomycin A and B) and ficellomycin contain an unusual 1-azabicyclo[3.1.0]hexane ring system, which has been reported to be the reason for theDNAcrosslinking abilities and cytotoxicity of these metabolites. Both families of natural products are produced by Streptomyces species, Streptomyces sahachiroi and Streptomyces ficellus, respectively. Up until recently, much of the work on these molecules has focused on the synthesis of these natural products or their corresponding analogs for in vitro investigations evaluating their DNA selectivity. While one of the most intriguing aspects of these natural products is their biosynthesis, progress made in this area was largely impeded by difficulties with obtaining a reliable culture method and securing a consistent source of these natural products. In this review, we will cover the discovery and biological activity of the azinomycins, their mode of action, related synthetic analogs and biosynthesis, and finish with a discussion on the less studied metabolite, ficellomycin.     

Effect of the pH of the medium on the chemical shifts in the PMR spectra and on the distribution of the π-electron density

The dependence of the chemical shift of the ring protons on the pH of the medium for a number of 3-hydroxyquinoline derivatives was studied by PMR spectroscopy. The regions of ionization of the molecules, which correspond to the ranges of acidic, neutral, and alkaline media, were found. In D₂O, 3-hydroxyquinoline is present only in the uncharged hydroxy form. The presence of intramolecular hydrogen bonding in 4-dimethylaminomethyl-3-hydroxyquinoline has a substantial effect on the character of the dependence of the chemical shift on the pH of the medium; the existence of separate protonation of the nitrogen atoms of the ring and the side chain of 4-dimethylaminomethyl-3-hydroxyquinoline was established. The distribution of the -electron density in the 3-hydroxyquinoline molecule is in good agreement with its chemical behavior during electrophilic substitution.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1540–1545, November, 1971.     

Effect of the pH of the medium on the chemical shifts in the PMR spectra and on the distribution of the π-electron density

The dependence of the chemical shifts of the ring protons on the pH of the medium for a number of 4-hydroxyquinoline derivatives was studied by means of PMR spectroscopy. The dipolar and uncharged hydroxy forms exist in equilibrium in aqueous solutions. The effect of intramolecular hydrogen bonding on the character of the dependence of the chemical shift on the pH of the medium in the case of 3-piperidinomethyl-4-hydroxyisoquinoline was investigated. The possibility of the separate protonation of the ring nitrogen and the side-chain nitrogen in 3-piperidinomethyl-4-hydroxyisoquinoline was established. The distribution of the -electron density in 4-hydroxyisoquinoline is in good agreement with its chemical behavior.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1546–1549, November, 1971     

On the theory underlying the Car-Parrinello method and the role of the fictitious mass parameter

The theory underlying the Car-Parrinello extended-Lagrangian approach to ab initio molecular dynamics (CPMD) is reviewed and reexamined using "heavy" ice as a test system. It is emphasized that the adiabatic decoupling in CPMD is not a decoupling of electronic orbitals from the ions but only a decoupling of a subset of the orbital vibrational modes from the rest of the necessarily coupled system of orbitals and ions. Recent work [J. Chem. Phys. 116, 14 (2002)] has pointed out that, due to the orbital-ion coupling that remains once adiabatic decoupling has been achieved, a large value of the fictitious mass mu can lead to systematic errors in the computed forces in CPMD. These errors are further investigated in the present work with a focus on those parts of these errors that are not corrected simply by rescaling the masses of the ions. It is suggested that any comparison of the efficiencies of Born-Oppenheimer molecular dynamics (BOMD) and CPMD should be performed at a similar level of accuracy. If accuracy is judged according to the average magnitude of the systematic errors in the computed forces, the efficiency of BOMD compares more favorably to that of CPMD than previous comparisons have suggested.     

On the volume-dependence of the index of refraction from the viewpoint of the complex dielectric function and the Kramers-Kronig relation

How indices of refraction n(omega) of insulating solids are affected by the volume dilution of an optical entity and the mixing of different, noninteracting simple solid components was examined on the basis of the dielectric function epsilon(1)(omega) + iepsilon(2)(omega). For closely related insulating solids with an identical composition and the formula unit volume V, the relation [epsilon(1)(omega) - 1]V = constant was found by combining the relation epsilon(2)(omega)V = constant with the Kramers-Kronig relation. This relation becomes [n(2)(omega) - 1]V = constant for the index of refraction n(omega) determined for the incident light with energy less than the band gap (i.e., h omega < E(g)). For a narrow range of change in the formula unit volume, the latter relation is well approximated by a linear relation between n and 1/V.     

From the Micro- to the Macro-: Managing the Conservation of the Warship,Vasa

Sweden's famous warship, Vasa, sank on her maiden voyage in August 1628, and remained on the bottom of Stockholm harbour for 333 years. Raised in 1961, she became the first large-scale wooden object to be treated with polyethylene glycol (PEG). In the summer of 2000 a number of acidic salt precipitations were noticed on the surface of the ship and on wooden artefacts in the storerooms. An international research project has been established to look into the causes of this problem and suggest possible re-treatments. Meanwhile projects are underway to monitor movements in the ship, to build a better support system, and to replace the thousands of iron bolts holding the structure together, while a sophisticated new climate system has recently been installed in the museum.