Our oceans, ourselves Helen Czerski Norton, 2023. 464 pp

An oceanographer's expansive portrait of the marine world captures its vitality and complexity.

New books, fresh for fall

From space weapons to mind reading, the books on this year's list tell tales of scientific transformation, balancing historical insights with urgent calls to action. Consider a transgender scientist's reflections on his legacy or tag along on a quest to save a tiny porpoise from extinction. Crack open a history of immunology or confront the future of artificial intelligence. Why would 12 men dine on purposely poisoned foods? Can we overcome "chronophobia"? What can termites teach us about technology? Read on to discover these answers and more. — Valerie Thompson

Ecology- and Bioassay-Guided Drug Discovery for Treatments of Tropical Parasitic Disease: 5α,8α-Epidioxycholest-6-en-3β-ol Isolated from the Mollusk Dolabrifera dolabrifera Shows Significant Activity against Leishmania donovani

An ecology- and bioassay-guided search employed to discover compounds with activity against tropical parasitic diseases and cancer from the opisthobranch mollusk, Dolabrifera dolabrifera, led to the discovery of antileishmanial properties in the known compound, 5α,8α-epidioxycholest-6-en-3β-ol (1). Compound 1 was identified through nuclear magnetic resonance spectroscopy (1H, 13C) and mass spectrometry. The compound was concentrated in the digestive gland of D. dolabrifera, but was not detected in other body parts, fecal matter or mucus. Compound 1 showed an IC50 of 4.9 μM towards the amastigote form of Leishmania donovani compared with an IC50 of 281 μM towards the control Vero cell line, a 57.3-fold difference, and demonstrated no measurable activity against Plasmodium falciparum, Trypanosoma cruzi, and the breast cancer cell line, MCF-7.

Ecology- and bioassay-guided drug discovery for treatments of tropical parasitic disease: 5alpha,8alpha-epidioxycholest-6-en-3beta-ol isolated from the mollusk Dolabrifera dolabrifera shows significant activity against Leishmania donovani

An ecology- and bioassay-guided search employed to discover compounds with activity against tropical parasitic diseases and cancer from the opisthobranch mollusk, Dolabrifera dolabrifera, led to the discovery of antileishmanial properties in the known compound, 5alpha,8alpha-epidioxycholest-6-en-3beta-ol (1). Compound 1 was identified through nuclear magnetic resonance spectroscopy (1H, 13C) and mass spectrometry. The compound was concentrated in the digestive gland of D. dolabrifera, but was not detected in other body parts, fecal matter or mucus. Compound 1 showed an IC50 of 4.9 microM towards the amastigote form of Leishmania donovani compared with an IC50 of 281 microM towards the control Vero cell line, a 57.3-fold difference, and demonstrated no measurable activity against Plasmodium falciparum, Trypanosoma cruzi, and the breast cancer cell line, MCF-7.

Malyngolide dimer, a bioactive symmetric cyclodepside from the panamanian marine cyanobacterium Lyngbya majuscula

Fractionation of the extract of the marine cyanobacterium Lyngbya majuscula collected from Panama led to the isolation of malyngolide dimer (1). The planar structure of 1 was determined using 1D and 2D NMR spectroscopy and HRESI-TOFMS. The absolute configuration was established by chemical degradation followed by chiral GC-MS analyses and comparisons with an authentic sample of malyngolide seco-acid (4). Compound 1 showed moderate in vitro antimalarial activity against chloroquine-resistant Plasmodium falciparum (W2) (IC(50) = 19 microM) but roughly equivalent toxicity against H-460 human lung cell lines. Furthermore, because the closely related cyanobacterial natural product tanikolide dimer (5) was a potent SIRT2 inhibitor, compound 1 was evaluated in this assay but found to be essentially inactive.

Antimalarial linear lipopeptides from a Panamanian strain of the marine cyanobacterium Lyngbya majuscula

As part of the Panama International Cooperative Biodiversity Groups (ICBG) project, two new (2, 4) and two known (1, 3) linear alkynoic lipopeptides have been isolated from a Panamanian strain of the marine cyanobacterium Lyngbya majuscula. Carmabin A (1), dragomabin (2), and dragonamide A (3) showed good antimalarial activity (IC50 4.3, 6.0, and 7.7 microM, respectively), whereas the nonaromatic analogue, dragonamide B (4), was inactive. The planar structures of all four compounds were determined by NMR spectroscopy in combination with mass spectrometry, and their stereoconfigurations were established by chiral HPLC and by comparison of their optical rotations and NMR data with literature values.

Antiplasmodial metabolites isolated from the marine octocoral Muricea austera

Bioassay-guided fractionation of the MeOH extract from the octocoral Muricea austera collected in the Pacific coast of Panama led to the isolation of eight compounds, including three tyramine derivatives (1-3), two steroidal pregnane glycosides (4, 5), and three sesquiterpenoids (6-8). Compounds 2-5 are new natural products, and their structures were determined on the basis of their spectroscopic data (HRMS, 1D and 2D NMR, and CD studies). The antiprotozoal activities of the natural compounds 1-8 as well as those of a series of synthetic glycosides (11-22) and tyramine derivatives (23-35) were evaluated in vitro against a drug-resistant Plasmodium falciparum and intracellular form of Trypanosoma cruzi.

Weakly antimalarial flavonol arabinofuranosides from Calycolpus warszewiczianus

Three new flavonol arabinosides (2-4) were isolated from the young leaves of Calycolpus warszewiczianus. The structures were determined as myricetin-3-O-alpha-L-3' '-acetylarabinofuranoside (2), myricetin-3-O-alpha-L-3' ',5' '-diacetylarabinofuranoside (3), and 5-galloylquercetin-3-O-alpha-L-arabinofuranoside (4). Molecular structures were elucidated using NMR spectroscopy in combination with IR and MS data. Two known compounds, myricetin-3-O-alpha-L-arabinofuranoside (1) and (-)-epi-catechin (5), were also isolated. The compounds were tested in vitro against a chloroquine-resistant strain of Plasmodium falciparum, Leishmania mexicana, and Trypanosoma cruzi parasites. Compound 4 demonstrated weak activity against a chloroquine-resistant strain of P. falciparum (14.5 microM), whereas none of the compounds demonstrated activity against L. mexicana and T. cruzi at the concentrations of 40 and 50 microg/mL, respectively, and no cytotoxicity was detected against mammalian cells below 100 microg/mL.

Caucanolides A-F, unusual antiplasmodial constituents from a colombian collection of the gorgonian coral Pseudopterogorgia bipinnata

Six new diterpenoids, caucanolides A-F (1-6), have been isolated from extracts of the gorgonian octocoral Pseudopterogorgia bipinnata collected near the Colombian Southwestern Caribbean Sea. The structures of 1-6 were elucidated by comprehensive analysis of spectroscopic data. The caucanolides showed in vitro antiplasmodial activity against the malaria parasite, Plasmodium falciparum. In addition to possessing structures based on novel carbon skeletons, one of these metabolites, caucanolide B (2), constitutes the only example from nature of a secondary metabolite possessing the N(1),N(1)-dimethyl-N(2)-acylformamidine functionality.

Antitrypanosomal activity of a novel norlignan purified from Nectandra lineata

Bioactivity-guided fractionation of a MeOH-EtOAc extract from the young leaves of Nectandra lineata (Lauraceae), using a Trypanosoma cruzi bioassay resulted in the isolation of a novel norlignan 3'-methoxy-3,4-methylenedioxy-4',7-epoxy-9-nor-8,5'-neolignan-9'-acetoxy (1), together with the known compound, 3'-methoxy-3,4-methylenedioxy-4'-7-epoxy-9-nor-8,5'-neolignan-7,8'-diene (2). Compounds 1 and 2 were shown to inhibit the growth of T. cruzi epimastigotes in axenic culture.

Leptolide, a new furanocembranolide diterpene from Leptogorgia alba

Six furanocembranolides (1-6) and one pseudopterolide (7) have been isolated from the octocorals Leptogorgia alba and Leptogorgia rigida, collected on the Pacific coast of Panama. Compound 1, named leptolide, has a new structure closely related to the neurotoxin lophotoxin (3). The X-ray structures of 1-3 were determined, and the absolute configurations of 2-7 are discussed. Compounds 1-7 were evaluated in vitro against drug-resistant Plasmodium falciparum.

Bielschowskysin, a gorgonian-derived biologically active diterpene with an unprecedented carbon skeleton

Bielschowskysin is a naturally occurring diterpene isolated from the Caribbean gorgonian octocoral Pseudopterogorgia kallos. Its highly oxygenated hexacyclic structure is based on a previously undescribed tricyclo[9.3.0.0(2,10)]tetradecane ring system that was established through spectroscopic analysis and X-ray crystallographic analysis. Bielschowskysin was shown to exhibit antimalarial activity against Plasmodium falciparum as well as strong anticancer activity against two human cancer cell lines.

Novel cassane and cleistanthane diterpenes from Myrospermum frutescens: absolute stereochemistry of the cassane diterpene series

Four new diterpenes (1-4) were isolated from the leaves of Myrospermum frutescens as minor constituents. Chagresnol (1), 6beta,18-diacetoxycassan-13,15-diene (2), and chagreslactone (3) possess cassane skeletons, while chagresnone (4) exhibits a cleistanthane skeleton. Molecular structures and their relative stereochemistries were elucidated using NMR spectroscopy in combination with UV, IR, and MS spectral data. Although compound 2 was previously reported as a synthetic product, we report its first isolation as a natural product. Derivative products (10-13) were obtained to test their activities against Chagas's disease. In addition, the absolute stereochemistry of the previously isolated cassane diterpene 5 from M. frutescens is presented.

Hydrosoluble formazan XTT: its application to natural products drug discovery for Leishmania

A colorimetric method for measuring the viability of Leishmania promastigotes is described that is based on the reduction of the tetrazolium salt, XTT, to a water-soluble formazan. Values obtained by the XTT method correlated well with parasite number (r=0.965) and with methods that rely upon the reduction of MTT or MTS (r=0.96 and 0.97, respectively). The IC(50) values obtained by XTT method with amphotericin-B, miltefosine and ketoconazole were similar to those previously reported by other methods. The XTT method proved to be a reliable and convenient method for the screening of methanolic extracts from 1059 plants and was used for the bioassay-guided fractionation of the alkaloid aegeline from Sarcorhachis naranjoana.

New cytotoxic naphthopyrane derivatives from Adenaria floribunda

Bioassay-guided fractionation of an EtOAc/MeOH extract of Adenaria floribunda young leaves using MCF-7, H-460, and SF-268 cancer cell lines yielded four new active compounds named adenaflorins A-D (1-4). Their chemical structures were determined by spectroscopic means. Adenaflorin A (1) was the most cytotoxic.

A novel DNA-based microfluorimetric method to evaluate antimalarial drug activity

This paper describes the development of a novel microfluorimetric assay to measure the inhibition of Plasmodium falciparum based on the detection of parasitic DNA by intercalation with PicoGreen. The method was used to determine parasite inhibition profiles and 50% inhibitory concentration values of known or potential antimalarial drugs. Values for parasite inhibition with known anti-malarial drugs using the PicoGreen assay were comparable with those determined by the standard method based upon the uptake of 3H-hypoxanthine and the Giemsa stain microscopic technique. The PicoGreen assay is rapid, sensitive, reproducible, easily interpreted, and ideally suited for screening of large numbers of samples for anti-malarial drug development.

Five new cassane diterpenes from Myrospermum frutescens with activity against Trypanosoma cruzi

Five novel cassane diterpenes (1-5) with activity against Trypanosoma cruzi were isolated from leaves of Myrospermum frutescens. The structures were determined as 18-hydroxycassan-13,15-diene (1), 6beta,18-dihydroxycassan-13,15-diene (2), 6beta-hydroxy-18-acetoxycassan-13,15-diene (3), 18-acetoxy-13,15-diene-19-cassanoic acid (4), and 6beta,13beta-dihydroxy-18-acetoxycassan-14(17),15-diene (5). Structures were elucidated by spectroscopic analysis (NMR and HRCIMS) and by the synthesis of derivatives 2a and 2b. Compounds 3 and 5 were more active against the extracellular form of the parasite (11 and 16 microM, respectively) than the intracellular forms, while compounds 1 and 2 were more active against the more clinically relevant intracellular forms of the parasite (17 microM). Compounds 1 and 2 were approximately 9-fold more toxic toward T. cruzi than toward human fibroblasts, the cell type that serves as the parasite's mammalian host cell.

Aporphine alkaloids from Guatteria spp. with leishmanicidal activity

Fractionation of Guatteria amplifolia yielded the alkaloids xylopine (1), nornuciferine (4), lysicamine (6), and laudanosine (5). Fractionation of Guatteria dumetorum yielded the alkaloids cryptodorine (2) and nornantenine (3). Compounds 1-4 demonstrated significant activity against Leishmania mexicana and L. panamensis. Xylopine (1) was among the most active compounds (LD 50 = 3 microM) and showed a 37-fold higher toxicity towards L. mexicana than macrophages, the regular host cells of Leishmania spp.

Bioactive constituents from three Vismia species

Bioassay-guided fractionation of the methanolic extracts of Vismia baccifera, V. jefensis, and V. macrophylla against human breast, CNS, and lung cancer cell lines resulted in the isolation of a new compound, ferruginin C (1), and seven known compounds, ferruginins A (2) and B (3), vismin (4), harunganin (5), vismione B (6), deacetylvismione H (7), and deacetylvismione A (8), as active constituents. In addition, bivismiaquinone (9) and vismiaquinone (10) were obtained as inactive constituents. The structure of ferruginin C was elucidated by spectroscopic means. Compounds 6-8 were the most active, and the cytotoxic activity of compounds 2-5 and 7 is reported for the first time.

Briarellins J-P and polyanthellin A: new eunicellin-based diterpenes from the gorgonian coral Briareum polyanthes and their antimalarial activity

A new chemical study of the hexane extract of the gorgonian Briareum polyanthes collected in Puerto Rico afforded 10 new diterpenes of the eunicellin class, briarellins 1-9 and polyanthellin A (10), along with the known diterpene briarellin D (11). The structures and relative stereochemistry of metabolites 1-10 were assigned on the basis of NMR studies, chemical methods, and comparisons to the spectral properties of 11. A reassessment of prior structural assignment for briarellin A and two known sclerophytin-type diterpenes, 13 and 14, is proposed. Antimalarial tests on 1-6 and 8-12 indicated that they were active against Plasmodium falciparum.

Differences in the topoisomerase I cleavage complexes formed by camptothecin and wakayin, a DNA-intercalating marine natural product

Wakayin is bispyrroloiminoquinone isolated from a Clavelina sp. ascidian by cytotoxicity directed fractionation. Like camptothecin, it has been found to inhibit the topoisomerase I catalyzed relaxation of supercoiled DNA. Wakayin enhanced cleavage complex formation at the same DNA sequences as camptothecin. Both compounds showed dose-related increases in cleavage complex formation, though wakayin's effect is attenuated at high concentrations. Wakayin is a string DNA binder. Wakayin also differed from camptothecin in that its cleavage complexes were much less stable than those of camptothecin in 0.5 M NaCl. Again in contrast to camptothecin, wakayin stabilized cleavage complexes poorly, if at all, at 0 degree C.

Construction and characterization of a bacteriophage T4 DNA polymerase deficient in 3'-->5' exonuclease activity

Bacteriophage T4 DNA polymerase has a proofreading 3'-->5' exonuclease that plays an important role in maintaining the accuracy of DNA replication. We have constructed a T4 DNA polymerase deficient in this exonuclease by converting Asp-219 to Ala. The exonuclease activity of the mutant T4 DNA polymerase has been reduced by a factor of at least 10(7), but it retains a polymerase activity whose kinetic parameters, kcat, Kd DNA, and Kd dATP, are very close to those of the wild-type enzyme. Bacteriophage T4 with the mutant polymerase gene has a markedly increased mutation frequency. Asp-219 in T4 DNA polymerase is within a sequence similar to those surrounding Asp residues previously shown to be essential for the exonuclease activities of the Klenow fragment of Escherichia coli DNA polymerase I (Asp-424), bacteriophage phi 29 DNA polymerase (Asp-66), and Saccharomyces cerevisiae DNA polymerase delta (Asp-405). Thus, these studies support the proposal that there are similar sequences in the active sites for the proofreading exonucleases of these and related DNA polymerases.

Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4

The DNA polymerase from the bacteriophage T4 is part of a multienzyme complex required for the synthesis of DNA. As a first step in understanding the contributions of individual proteins to the dynamic properties of the complex, e.g., turnover, processivity, and fidelity of replication, the minimal kinetic schemes for the polymerase and exonuclease activities of the gene 43 protein have been determined by pre-steady-state kinetic methods and fit by computer simulation. A DNA primer/template (13/20-mer) was used as substrate; duplexes that contained more single-strand DNA resulted in nonproductive binding of the polymerase. The reaction sequence features an ordered addition of 13/20-mer followed by dATP to the T4 enzyme (dissociation constants of 70 nM and 20 microM) followed by rapid conversion (400 s-1) of the T4.13/20-mer.dATP complex to the T4.14/20-mer.PPi product species. A slow step (2 s-1) following PPi release limits a single turnover, although this step is bypassed in multiple incorporations (13/20-mer-->17/20-mer) which occur at rates > 400 s-1. Competition between correct versus incorrect nucleotides relative to the template strand indicates that the dissociation constants for the incorrect nucleotides are at millimolar values, thus providing evidence that the T4 polymerase, like the T7 but unlike the Klenow fragment polymerases, discriminates by factors > 10(3) against misincorporation in the nucleotide binding step. The exonuclease activity of the T4 enzyme requires an activation step, i.e., T4.DNA-->T4.(DNA)*, whose rate constants reflect whether the 3'-terminus of the primer is matched or mismatched; for matched 13/20-mer the constant is 1 s-1, and for mismatched 13T/20-mer, 5 s-1. Evidence is presented from crossover experiments that this step may represent a melting of the terminus of the duplex, which is followed by rapid exonucleolytic cleavage (100s-1). In the presence of the correct dNTP, primer extension is the rate-limiting step rather than a step involving travel of the duplex between separated exonuclease and polymerase sites. Since the rate constant for 13/20-mer or 13T/20-mer dissociation from the enzyme is 6 or 8 s-1 and competes with that for activation, the exonucleolytic editing by the enzyme alone in a single pass is somewhat inefficient (5 s-1/(8 s-1+5 s-1)), ca. 40%. Consequently, a major role for the accessory proteins may be to slow the rate of enzyme.substrate dissociation, thereby increasing overall fidelity and processivity.

Protein-DNA cross-linking demonstrates stepwise ATP-dependent assembly of T4 DNA polymerase and its accessory proteins on the primer-template

T4 DNA polymerase, the 44/62 and 45 polymerase accessory proteins, and 32 single-stranded DNA-binding protein catalyze ATP-dependent DNA synthesis. Using DNA primers with cross-linkable residues at specific positions, we obtained structural data that reveal how these proteins assemble on the primer-template. With the nonhydrolyzable ATP analog ATP gamma S, assembly of the 44/62 and 45 proteins on the primer requires 32 protein but not polymerase. ATP hydrolysis changes the position and intensity of cross-linking to each of the accessory proteins and allows cross-linking of polymerase. Our data indicate that the initial binding of the three accessory proteins and ATP to a 32 protein-covered primer-template is followed by ATP hydrolysis, binding of polymerase, and movement of the accessory proteins to yield a complex capable of processive DNA synthesis.

Steady-state kinetics of bovine striatal tyrosine hydroxylase

The steady-state kinetics of tyrosine hydroxylase [L-tyrosine, tetrahydropteridine: oxygen oxidoreductase (3-hydroxylating); EC 1.14.16.2] frequently exhibits complex features which confound interpretation of the results. Using an assay-enzyme system which is essentially devoid of the major mitigating kinetic features, a comprehensive kinetics data base has been compiled. The studies employed L-tyrosine, 5,6,7,8-tetrahydrobiopterin, and oxygen as substrates, and 3-(3',4'-dihydroxyphenyl)L-alanine, a deazapterin, 3-iodo-L-tyrosine, and dopamine as product, substrate analogue, and product analogue inhibitors, respectively. All three reactants were varied pairwise, and all inhibitors (except dopamine) were tested with each of the three substrates as variable substrate. The entire data base was interpreted exclusively in terms of models for classic saturation kinetics of enzyme catalysis, providing an internally consistent kinetic model and evidence for a sequential mechanism with partially ordered sequences for substrate addition and product release. Some possible mechanisms and experimental variables relating these results to more complex kinetics of tyrosine hydroxylase are considered briefly.