Reflections on the intriguing occurrence of some recently isolated natural products as racemates and scalemic mixtures.

This review continues our interest in the intriguing reports of a variety of new racemic natural products (at least 11 in the past 4 years). These include the polyphenolic racemate galewone, the polycyclic prenylated acylphloroglucinol garcinielliptone; variecolortide, a combination of an anthraquinone and a isochinulin-type alkaloid; the isoindoline alkaloid irpexine, the new hybrid phenylproanoid asarone; colletopyandione an indolydenepyradione; the enantiomerically enriched (scalemic) neolignans, gardenifolins; and meroterpenoid pabmaragramin in addition to some marine lipids. We also present a recent biomimetic synthesis of the polyketide preuisolactone A; synthesis of the polyketide spiromamakone A, which also corrected the proposed structure of another metabolite as identical to spiromamakone A; and the melicolones A and B. The continuing reports of natural racemates provoke speculation as to their role in the producing organism.

The enduring legacy of Koji Nakanishi's research on bioorganic chemistry and natural products. Part 1: Isolation, structure determination and mode of action.

In this brief review on Koji Nakanishi's remarkable career in natural products chemistry, we have highlighted a number of his accomplishments that illustrate the broad diversity of his interests. These include the isolation, structure determination, and biological mechanism of action of many natural products including the triterpenoid pristimerin; the diterpenoid ginkgolides; insect and crustacean molting hormones; phytoalexins; the toxic red tide principle brevetoxin; the vanadium tunicate pigments; philanthotoxin from killer wasps; antisickling agents; mitomycin DNA adducts; insect antifeedants; a mitotic hormone, the small molecule fish attractants from the sea anemone; new isolation and purification technologies; molecular chemistry of vision; age-related macular degeneration; and the development of the exciton circular dichroism (CD) chirality method for microscale determination of absolute configuration of natural products and chirality of other chiral molecules and supramolecular assembly.

Pimarane diterpenes: Natural source, stereochemical configuration, and biological activity.

Plants and fungi are seemingly inexhaustible sources of interesting natural products with remarkable structural and biological diversity. One of the most important groups is the terpenes, ubiquitous natural products that are generated by 2 now well-established biosynthetic pathways: the older mevalonate and the more recently discovered 1-deoxyxylulose-5-phosphate. Among the diterpenes, the pimarane diterpenes are a very representative subgroup with several and interesting biological activities resulting from different functional group modifications. In this review, we outline the method of their structure determination, mainly spectroscopic results, their absolute configuration, and structure-activity relationships, were reported, as well as the mode of action for selected examples from plants, marine organisms, and fungi. The pimarane, isopimarane, and ent-pimarane diterpenes covered in this review have a wide range of biological activities including antimicrobial, antifungal, antiviral, phytotoxic, phytoalexin, cytotoxicity, and antispasmodic and relaxant effects.

Biomimetic syntheses of racemic natural products.

Racemic natural products are rarely produced in plants and microorganisms and are thought to be the result of nonenzymatic, spontaneous reactions. These compounds are often highly complex with multiple contiguous chiral centers that present a challenge to organic synthesis. Formation of these racemates often occurs by cyclization reactions that can generate multiple stereocenters from achiral precursors. Biomimetic synthesis of these racemic natural products provides support for their proposed nonenzymatic spontaneous biosynthesis. These elegant syntheses also provide scalable and efficient routes to these complex natural products. Although the number of reported racemic natural products is relatively low, an isolated natural product that has a very small optical rotation has been shown to be a true racemate. Thus, the occurrence of racemic natural products could be more common than thought.

Circular dichroism analysis of the calicheamicin-DNA interaction revisited.

Calicheamicin, γ1I, is a remarkable DNA binding-cleaving, enediyne-containing, natural product that exhibits potent antitumor activity. In this study, we used electronic circular dichroism spectroscopy to monitor potential drug-induced DNA conformational changes and DNA induced conformational changes in the calicheamicin aglycone. Three DNA dodecamer sequences were examined: one containing a primary TCCT binding/cleavage site and two dodecamers containing less prominent CTCT and TCTC sites. The binding was monitored by taking advantage of the drug's unique negative exciton couplet (-313nm/+275nm) in phosphate buffer/ethanol 10%. Specifically the CD analysis focused at the longest wavelength region around 313nm where there is no interference by the positive CD contributions of the DNA. Upon binding at a DNA/drug ratio of 1/1.2 and 1/2.7 a slight red shift from 313nm to 319nm was observed. At a ratio of 1/1.2, the CE intensity remained practically unchanged from that of free drug, which indicates no conformational changes in the bound aglycone itself. A larger amount of drug, at a molar ratio of DNA/drug of 1/2.7 but especially at 1/6 and up to 1/10, however, caused a surprisingly distinct decrease in the intensity at this negative CD band and a further small red-shift to 322nm, evidence for non-specific binding.

Recent Advances in Stereoselective Drug Targeting.

Reviewed here are some recent examples of medically important protein targets for which stereoselective drugs have been identified. These include heat shock protein 90 (Hsp90) inhibitors as anticancer agents; transient receptor potential vanilloid type 1 antagonists as new analgesics; stereospecific inhibition of human mutT homolog MTH1 for cancer treatment; the stereoselective binding of R- and S-propranolol by the α1-acid glycoprotein transporter; metallohelical complexes that are nonpeptide α-helical mimetics that enantioselectively target Aß amyloid for the treatment of Alzheimer's disease; metallohelical assemblies with promising antimicrobial activity that enantioselectively target DNA of resistant bacteria; nonpeptide α-helical metallohelices that target the DNA of cisplatin-resistant cancer cells; diastereomeric selectivity of phenanthriplatin-guanine adducts; and phenazine biosynthetic enzyme active sites that can host both enantiomers of a racemic ligand simultaneously.

Biological stereoselectivity of atropisomeric natural products and drugs.

Selected examples of natural product and drug atropisomers that exhibit stereoselectivity towards receptor and enzyme targets are reviewed. The atropisomeric preference of the receptors and enzyme binding domains makes these agents attractive molecules for drug development in the treatment of various diseases. Included are commonly recognized atropisomers containing a chiral biaryl axis along with some less common examples of atropisomers without a biaryl axis. The biological targets include: antiapoptotic proteins; bacteria; microtubules; kinases; vasopressin receptors; a G-protein coupled receptor related to obesity; monocarboxylate transporters; tachykinin NK1 -receptors; cyclooxygenase-1 and squalene synthase.

Synthesis of antioxidants for prevention of age-related macular degeneration.

Photooxidation of A2E may be involved in diseases of the macula, and antioxidants could serve as therapeutic agents for these diseases. Inhibitors of A2E photooxidation were prepared by Mannich reaction of the antioxidant quercetin. These compounds contain water-solubilizing amine groups, and several were more potent inhibitors of A2E photooxidation than quercetin.

Plasmonic chiroptical response of silver nanoparticles interacting with chiral supramolecular assemblies.

Silver nanoparticles were prepared in aqueous solutions of chiral supramolecular structures made of chiral molecular building blocks. While these chiral molecules display negligible circular dichroism (CD) as isolated molecules, their stacking produced a significant CD response at room temperature, which could be eliminated by heating to 80 °C due to disordering of the stacks. The chiral stack-plasmon coupling has induced CD at the surface plasmon resonance absorption band of the silver nanoparticles. Switching between two plasmonic CD induction mechanisms was observed: (1) Small Ag nanoparticles coated with large molecular stacks, where the induced plasmonic CD decayed together with the UV molecular CD bands on heating the solution, indicating some type of electromagnetic or dipole coupling mechanism. (2) Larger Ag nanoparticles coated with about a monolayer of molecules exhibited induced plasmonic CD that was temperature-independent. In this case it is estimated that the low chiroptical response of a molecular monolayer is incapable of inducing such a large chiroptical effect, and a model calculation shows that the plasmonic CD response may be the result of a slight chiral shape distortion of the silver nanoparticles.

Structural and conformational features relevant to the anti-tumor activity of calicheamicin γ 1I.

The structural and conformational features of the potent 10-membered enediyne-containing calicheamicin γ 1I that account for its remarkable DNA site-specific binding and cleavage are reviewed. A variety of spectroscopic and biophysical techniques were used to gain insight into the binding and stereospecific DNA cleavage of this potent antitumor agent. These include gel-shift cleavage assays, atom transfer NMR experiments, drug-DNA conformational studies, circular dichroism, and capillary electrophoresis. Computational descriptions are described for the DNA binding and cleavage of calicheamicin and its activated transient intermediates based on density functional and molecular mechanics calculations. In addition, the structure and clinical utility of calicheamicin immunoconjugates for antibody-targeted chemotherapy is presented.

Calicheamicin γ1(I) and phenyl tert-butyl nitrone (PBN): observation of a kinetic isotope effect by an ESR study.

ESR study of enediyne calicheamicin gamma(1)(I) with phenyl tert-butyl nitrone (PBN) gave a significant kinetic isotope effect (k(H)/k(D) = 1.8) for the formation of the phenyl radical PBN monoadducts.

Role of environmental factors on the structure and spectroscopic response of 5'-DNA-porphyrin conjugates caused by changes in the porphyrin-porphyrin interactions.

We have explored the utility, strength, and limitation of through-space exciton-coupled circular dichroism in determination of the secondary structure of optically active chromophoric nanoarrays using the example of end-capped porphyrin- and metalloporphyrin-oligodeoxynucleotide conjugates. We put special emphasis on the explanation of the origin and significance of the distinctive multiple bands in the CD spectra (trisignate and tetrasignate CD bands). Such CD profiles are often observed in chiral aggregates or multichromophoric arrays but have never before been studied in detail. We found that variation of temperature and ionic strength has a profound effect on the geometry of the porphyrin-DNA conjugates and thus the nature of electronic interactions. At lower temperatures and in the absence of NaCl all three 5'-DNA-porphyrin conjugates display negative bisignate CD exciton couplets of variable intensity in the Soret region resulting from through-space interaction between the electric transition dipole moments of the two end-capped porphyrins. As the temperature is raised these exciton couplets are transformed into single positive bands originating from the porphyrin-single-strand DNA interactions. At higher ionic strengths and low temperatures, multisignate CD bands are observed in the porphyrin Soret region. These CD signature bands originate from a combination of intermolecular, end-to-end porphyrin-porphyrin stacking between duplexes and porphyrin-DNA interactions. The intermolecular aggregation was confirmed by fluorescence and absorption spectroscopy and resonance light scattering. DeVoe theoretical CD calculations, in conjunction with molecular dynamics simulations and Monte Carlo conformational searches, were used to mimic the observed bisignate exciton-coupled CD spectra as well as multiple CD bands. Calculations correctly predicted the sign and shape of the experimentally observed CD spectra. These studies reveal that the exciton-coupled circular dichroism is a very useful technique for the determination of the structure of optically active arrays.

Synthesis and characterization of water-soluble free-base, zinc and copper porphyrin-oligonucleotide conjugates.

We describe the synthesis and characterization of a series of water-soluble free-base, zinc, and copper porphyrin-oligonucleotide (ODN) conjugates. A non-charged tetraarylporphyrin was directly attached to the 5'-position of thymine via a short amide linker. Such a linker should allow for rigid connection to the adjacent nucleobases, thus increasing the sensitivity for monitoring conformational changes of the ODNs by electronic circular dichroism due to capping effects or ligand binding. Two complementary synthetic approaches have been used to incorporate porphyrin chromophores into the DNA. In the first approach a porphyrin carboxylic acid is conjugated to 5'-amino-ODN. In the second approach the phosphoramidite of the porphyrin-amido-thymidine is coupled to 5'-hydroxy-ODN using standard automated phosphoramidite chemistry. In both cases a spontaneous metallation of the free-base porphyrin in porphyrin-DNA conjugates was observed during the porphyrin-DNA conjugate cleavage from the solid support and its consequent deprotection using concentrated aqueous ammonia. Zinc and copper porphyrin-DNA conjugates were isolated by HPLC and characterized together with the anticipated free-base porphyrin-DNA conjugate. Authentic zinc and copper porphyrin-DNA conjugates were intentionally prepared from intentionally metallated porphyrins to compare their spectroscopic and HPLC characteristics with isolated metallospecies and to confirm the spontaneous metallation.

Biochemical and biophysical characterization of inhibitor binding to caspase-3 reveals induced asymmetry.

Activation of the caspase family of cysteine proteases results in the deregulation of cellular homeostasis and apoptosis. This deregulation is a key factor in the development of Alzheimer's disease, Parkinson's disease, and cancer. Thus, the caspases are important drug targets for the therapeutic intervention of a number of pathological states involving inflammation and apoptosis. In this article, we report the results of inhibition kinetics and binding studies utilizing fluorescence spectroscopy and isothermal titration calorimetry to characterize the mechanism of interaction of caspase-3 with three different classes of inhibitors: peptidomimetics, isatins, and pyrimidoindolones. The peptidomimetics and pyrimidoindolones bind to both active sites of the caspase-3 homodimer with equal affinity and favorable enthalpic and entropic binding contributions. Enzyme activity is abolished when both active sites are occupied with the above inhibitors. In contrast, the isatins bind to caspase-3 with significant heat release (-12 kcal/mol) and negative entropy. In addition, enzyme activity is abolished upon isatin binding to one active site of the homodimer resulting in half-site reactivity. Our studies provide important mechanistic insight into inhibitor interactions with caspase-3 and a way to characterize inhibitor interactions that may not be readily apparent from the crystal structure.

Development of an HPLC assay for Staphylococcus aureus sortase: evidence for the formation of the kinetically competent acyl enzyme intermediate.

Many bacterial surface proteins containing an LPXTG motif are anchored to the cell wall peptidoglycan by catalysis with the thiol transpeptidase sortase. The transpeptidation and hydrolysis reactions of sortase have been proposed to proceed through a common acyl enzyme intermediate. The reactions of Staphylococcus aureus sortase with fluorogenic substrate Abz-LPETG-Dnp in the presence or absence of triglycine were characterized in this study to gain additional insight into the kinetic mechanism of sortase. We report here the development of a reverse-phase HPLC assay to identify and characterize sortase reaction intermediates. The HPLC results provide for the first time clear evidence for the formation of a kinetically competent acyl enzyme intermediate during the overall transpeptidation reaction. The results also suggest that sortase undergoes an unexpected intramolecular acyl transfer reaction in the absence of a nucleophile. The significance of this type of HPLC assay as a tool to study enzyme mechanism is discussed.

Spin-trapping of the p-benzyne intermediates from ten-membered enediyne calicheamicin gamma1I.

In the presence of thiols, the ten-membered-ring enediyne calicheamicin gamma1I generates a p-benzyne biradical that initiates oxidative cleavage of double-stranded DNA. Application of spin-trapping has successfully provided ESR and mass spectroscopic evidence for the formation of the monoadducts with phenyl tert-butyl nitrone (PBN). [reaction: see text].

Porphyrins conjugated to DNA as CD reporters of the salt-induced B to Z-DNA transition.

The porphyrin chromophore incorporated at the 5'-position of an oligonucleotide allows the simultaneous detection of the B- to Z-DNA transition via the porphyrin Soret band circular dichroism exciton couplet signal around 420 nm and the oligonucleotide CD region below 300 nm, at micromolar concentrations.