Structure elucidation of phase I metabolites of the microtubule perturbagens: ceratamines A and B.

The heterocyclic alkaloids, ceratamines A and B, are isolates from a marine Pseudoceratina sp. sponge. They behave as antimitotic agents, with IC50 values in the low micromolar range. The mechanism of this activity involves the disruption of microtubule dynamics; therefore, the ceratamines are of great interest in cancer drug discovery. Studies of in vitro metabolism were performed using rat liver microsomes to begin to understand the pharmacokinetics of these unique natural products. A total of eight metabolites were identified using UV and LC-MS/MS techniques. The majority of metabolites were formed as a result of various demethylation reactions. The formation of two metabolites, M1 and M3, involved monooxygenation, most likely on the aromatic ring, however the exact structure has not been determined. UV absorbance revealed a hypsochromic shift as a result of monooxygenation, an observation that may suggest the loss of aromaticity; however, further investigation is required. The structures of two major metabolites of ceratamine B, M4 and M6, were confirmed by (1)H NMR spectroscopy. These metabolites formed as a result of demethylation at the methoxy and aminoimidazole, respectively.

Structure-activity relationship studies of sulfonylpiperazine analogues as novel negative allosteric modulators of human neuronal nicotinic receptors.

Neuronal nicotinic receptors have been implicated in several diseases and disorders such as autism, Alzheimer's disease, Parkinson's disease, epilepsy, and various forms of addiction. To understand the role of nicotinic receptors in these conditions, it would be beneficial to have selective molecules that target specific nicotinic receptors in vitro and in vivo. Our laboratory has previously identified novel negative allosteric modulators of human α4ß2 (Hα4ß2) and human α3ß4 (Hα3ß4) nicotinic receptors. The effects of novel sulfonylpiperazine analogues that act as negative allosteric modulators on both Hα4ß2 nAChRs and Hα3ß4 nAChRs were investigated. This work, through structure-activity relationship (SAR) studies, describes the chemical features of these molecules that are important for both potency and selectivity on Hα4ß2 nAChRs.

Synthesis and DNA-binding affinity studies of glycosylated intercalators designed as functional mimics of the anthracycline antibiotics.

Anthracycline antibiotics such as daunomycin (Dauno) and doxorubicin (Dox) are well-known clinically used cancer chemotherapeutics, which, among other mechanisms, bind to DNA, thereby triggering a cascade of biological responses leading to cell death. However, anthracyclines are cardiotoxic, and drug resistance develops rapidly, thus limiting their clinical use. We report here the synthesis and DNA-binding affinity of a novel class of functional anthracycline mimetics consisting of an aromatic moiety linked to a carbohydrate (1-12). In the targets, the aromatic core consists of a 2-phenylbenzo[b]furan-3-yl, 2-phenylbenzo[b]thiophen-3-yl, 1-tosyl-2-phenylindol-3-yl, or 2-phenylindol-3-yl group that is bound to one of three aminosugars (daunosamine, acosamine, or 4-amino-2,3,4,6-tetradeoxy-alpha-l-hexopyranoside) via a propargyl linker. The DNA binding affinity of these twelve compounds has been evaluated by using both direct and indirect fluorescence measurements. Compared to Dauno and Dox, the DNA binding affinity of these analogues is weaker. However, both aromatic and aminosugar motifs are critical to DNA binding, with more influence coming from the structural features of the aromatic portion.

A direct and efficient total synthesis of the tubulin-binding agents ceratamine A and B; use of IBX for a remarkable heterocycle dehydrogenation.

The total synthesis of the tubulin-binding agents ceratamine A and B is reported, along with des-methyl analogs, via a synthetic route that is high-yielding and operationally efficient. The synthetic route involved a Beckmann rearrangement to form an azepine ring precursor, a Knoevenagel condensation to install the benzylic side chain, and an effective imidazole annulation onto an alpha-aminoketone precursor with a protected S-methylisothiourea. Final dehydrogenation proved remarkably facile using IBX.

Nanoscale structure and dynamics of DNA.

DNA is depicted in elementary chemistry and biology texts as a perfect double helix; but local structural variations and nanoscale motions within the double helix are critical for its ability to be packaged, recognized, and transcribed. DNA is becoming a favored nanoscale assembly tool due to the precise pairing of complementary strands that in principle can bring nanoscale objects within a well-defined distance of each other. However, future nanotechnology applications of DNA need to take into account its variable nanoscale structural and dynamic properties, especially in terms of its solvent shell and counterions. This article highlights efforts of the authors to (1) interrogate nanoscale structures of DNA using nanoparticles and (2) measure the dynamic nature of DNA over six orders of magnitude in time, using a fluorescent reporter in the base stack.

Total synthesis of the eupomatilones.

Full details of the total syntheses of five members of the eupomatilone family of lignans are reported.

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.

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.

Total synthesis of gymnoconjugatins A and B.

Convergent and efficient syntheses of the microbial natural products gymnoconjugatin A and B are reported and were based on a linchpin coupling strategy using a boron/tin hetero-bis-metallated butadiene system.

Synthesis of L-daunosamine and L-ristosamine glycosides via photoinduced aziridination. Conversion to thioglycosides for use in glycosylation reactions.

Application of photoinduced acylnitrene aziridination to the syntheses of L-daunosamine and L-ristosamine glycosides is reported. Photoreaction of methyl 4-O-azidocarbonyl-2,3,6-trideoxy-L-hex-2-enopyranosides, followed by aziridine opening, leads to 3-amino-3-N-,4-O-carbonyl-2,3,6-trideoxy precursors to the aminosugar methyl glycosides. Conversion of these precursors to their thioglycoside analogues followed by N-acetylation of the carbamate moiety permits high yielding and, in some cases, stereoselective glycosylations using the 1-benzenesulfinylpiperidine-triflic anhydride activation method developed by Crich and co-workers. Glycosylations involving activation with N-iodosuccinimide and silver triflate were also successful, but the stereoselectivities of these reactions in general were lower.

Role of monovalent counterions in the ultrafast dynamics of DNA.

This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.

Cellular effects induced by the antitumor agent azinomycin B.

Studies on the mechanism of action of the antitumor agent azinomycin B in vitro suggest that the drug elicits its lethal effects by the formation of interstrand crosslinks within the major groove of DNA. Here, we demonstrate the biological effects of the drug in vivo. Fluorescence imaging revealed localization of azinomycin B in the nuclear region of yeast. Moreover, experiments with oligonucleotide microarrays examined the effects of the drug across the yeast transcriptome. The results demonstrated a robust DNA damage response that supports the proposed role of the drug as a covalent DNA modifying agent. RT-PCR analysis validated the gene changes, and flow cytometry of azinomycin-treated yeast cells demonstrated a phenotypic S phase shift consistent with transcriptional effects.

Ultrafast dynamics in DNA: "fraying" at the end of the helix.

The dynamics of the electric fields in the interior of DNA are measured by using oligonucleotides in which a native base pair is replaced by a dye molecule (coumarin 102) whose emission spectrum is sensitive to the local electric field. Time-resolved measurements of the emission spectrum have been extended to a six decade time range (40 fs to 40 ns) by combining results from time-correlated photon counting, fluorescence up-conversion, and transient absorption. Recent results showed that when the reporter is placed in the center of the oligonucleotide, the dynamics are very broadly distributed over this entire time range and do not show specific time constants associated with individual processes (Andreatta, D.; et al. J. Am. Chem. Soc. 2005, 127, 7270). This paper examines an oligonucleotide with the reporter near its end. The broadly distributed relaxation seen before remains with little attenuation. In addition, a new relaxation with a well-defined relaxation time of 5 ps appears. This process is assigned to the rapid component of "fraying" at the end of the helix.

Total synthesis of strobilurin B using a hetero-bis-metallated pentadiene linchpin.

An efficient, six-step stereocontrolled total synthesis of the antifungal agent strobilurin B is reported and was based on a convergent bi-directional coupling featuring a hetero-bis-1,4-metallated pentadiene system as the linchpin.

Total synthesis of lucilactaene, a cell cycle inhibitor active in p53-inactive cells.

Hetero-bis-metalated 1,3-butadiene is employed in the lynchpin coupling of synthetic fragments of the side chain of the antitumor agent, lucilactaene. Sequential Stille and Suzuki-Miyaura couplings interpolate this unique boron/tin diene into the pentaene chain. The total synthesis of lucilactaene was accomplished efficiently, in just eight linear steps.

Effect of protein binding on ultrafast DNA dynamics: characterization of a DNA:APE1 complex.

Synthetic oligonucleotides with a fluorescent coumarin group replacing a basepair have been used in recent time-resolved Stokes-shift experiments to measure DNA dynamics on the femtosecond to nanosecond timescales. Here, we show that the APE1 endonuclease cleaves such a modified oligonucleotide at the abasic site opposite the coumarin with only a fourfold reduction in rate. In addition, a noncatalytic mutant (D210N) binds tightly to the same oligonucleotide, albeit with an 85-fold reduction in binding constant relative to a native oligonucleotide containing a guanine opposite the abasic site. Thus, the modified oligonucleotide retains substantial biological activity and serves as a useful model of native DNA. In the complex of the coumarin-containing oligonucleotide and the noncatalytic APE1, the dye's absorption spectrum is shifted relative to its spectrum in either water or within the unbound oligonucleotide. Thus the dye occupies a site within the DNA:protein complex. This result is consistent with modeling, which shows that the complex accommodates coumarin at the site of the orphaned base with little distortion of the native structure. Stokes-shift measurements of the complex show surprisingly little change in the dynamics within the 40 ps-40 ns time range.

Asymmetric total synthesis of dibenzocyclooctadiene lignan natural products.

[structure: see text] Full details of the asymmetric total syntheses of the dibenzocyclooctadiene lignans interiotherin A, angeloylgomisin R, gomisin O, and gomisin E (epigomisin O) are presented. The syntheses were based on a unified synthetic strategy involving a novel crotylation using the Leighton auxiliary that occurred with excellent asymmetric induction (>98:2 enantiomeric ratio), a diastereoselective hydroboration/Suzuki-Miyaura coupling reaction sequence, and an atropdiastereoselective biarylcuprate coupling, both of which occurred with total (>20:1) stereocontrol. The syntheses were achieved in six to eight steps from simple aromatic precursors.

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.

Power-law solvation dynamics in DNA over six decades in time.

Time-resolved Stokes shifts in a dye-containing oligonucleotide have been observed over the entire time range from 40 fs to 40 ns. The dynamics fit to a power law with a small exponent of 0.15. Similar relaxation has been seen in proteins but has not been anticipated in DNA. Distinct relaxation components due to specific subcomponents of the system, bulk water, bound water, counterions, backbone, bases, and so on, are not found. The various subcomponents may be so strongly coupled that their motions cannot be treated separately.