Key structural features of cis-cinnamic acid as an allelochemical

1-O-cis-cinnamoyl-β-d-glucopyranose is one of the most potent allelochemicals isolated from Spiraea thunbergii Sieb. It is suggested that it derives its strong inhibitory activity from cis-cinnamic acid, which is crucial for phytotoxicity. It was synthesized to confirm its structure and bioactivity, and also a series of cis-cinnamic acid analogues were prepared to elucidate the key features of cis-cinnamic acid for lettuce root growth inhibition. The cis-cyclopropyl analogue showed potent inhibitory activity while the saturated and alkyne analogues proved to be inactive, demonstrating the importance of the cis-double bond. Moreover, the aromatic ring could not be replaced with a saturated ring. However, the 1,3-dienylcyclohexene analogue showed strong activity. These results suggest that the geometry of the C–C double bond between the carboxyl group and the aromatic ring is essential for potent inhibitory activity. In addition, using several light sources, the photostability of the cinnamic acid derivatives and the role of the C–C double bond were also investigated.     

Phytotropins: Conformational requirements for the abolition of the root geotropic response

Compounds of the phytotropin class have been assessed for possible conformational requirements with respect to their ability to aftect the root geotropic response. It is shown that part of the molecule may need to adopt a planar configuration, and evidence is adduced which indicates that the remainder of the molecule may also have conformational requirements which need further definition. It is suggested that molecules which favour a conformation such that the aromatic ring which bears the carboxyl function is out of plane with the remainder of the molecule may have activity. Coplanarity of the carboxyl group with the ring to which it is attached is not a prerequisite for activity.     

Theoretical study of the catalytic reaction mechanism of MndD

Manganese-dependent homoprotocatechuate 2,3-dioxygenase (MndD) is an enzyme taking part in the catabolism of aromatic compounds in the environment. It uses molecular oxygen to perform an extradiol cleavage of the ring of the ortho-dihydroxylated aromatic compound homoprotocatechuate. A theoretical investigation of the reaction path for MndD was performed using hybrid density functional theory with the B3LYP functional, and a catalytic mechanism has been suggested. Models of different size were built from the crystal structure of the enzyme and were used in the search for intermediates and transition states. It was found that the substrate first binds at the active site as a monoanion. Next the dioxygen is bound, forming a hydroperoxo intermediate. The O–O bond, activated in this way undergoes homolytic cleavage leading to an oxyl and then to an extra epoxide radical with subsequent opening of the aromatic ring. The lactone ring is then hydrolyzed by the Mn-bound OH group, and the final product is obtained in the last reaction steps. Alternative reaction paths were considered, and their calculated barriers were found to be higher than for the suggested mechanism. The selectivity between the extra- and intra-cleavage pathways was found to be determined by the barriers for the decay of the radical state.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis

The expression of pathogenicity-related extracellular proteases, namely, gelatinase and serine protease, in Enterococcus faecalis is positively regulated by a quorum-sensing system mediated by an autoinducing peptide called gelatinase biosynthesis-activating pheromone (GBAP). GBAP is an 11-amino-acid-residue cyclic peptide containing a lactone linkage. To study the structure-activity relationship of GBAP, we synthesized a series of GBAP analogues and evaluated their activities by a gelatinase-inducing assay and newly developed receptor-binding assays in which fluorescence-labeled peptides bound onto the FsrC-overexpressing Lactococcus lactis cell surface were observed by fluorescent microscopy and quantified by using a fluorophotometer. Alanine-scanning analysis of GBAP showed that the entire ring region was involved in the GBAP agonist activity, while side chains of the tail region were not strictly recognized. The alanine substitution of Phe⁷ or Trp¹⁰ almost abolished their receptor-binding abilities and GBAP agonist activities, suggesting that these two aromatic side chains are strongly involved in receptor interaction and activation. Furthermore, the Trp¹⁰ substitution with natural and unnatural aromatic amino acids, except pentafluorophenylalanine, caused no loss of agonist activity. This suggested the importance of a negative electrostatic potential created by an π-electron cloud on the aromatic ring surface. Structural analysis of GBAP with nuclear magnetic resonance spectroscopy revealed that the ring region adopted a hairpin-like fold and was tightly packed into a compact form. The side chain of Trp¹⁰ was partially buried in the core structure, contributing to the stabilization of the compact form, while that of Phe⁷ was extended from the core structure into the solvent and was probably directly involved in receptor binding.     

Exploring the molecular basis of action of ring D aromatic steroidal antiestrogens

Salpichrolides are natural plant steroids that contain an unusual six‐membered aromatic ring D. We recently reported that some of these compounds, and certain analogs with a simplified side chain, exhibited antagonist effects toward the human estrogen receptor (ER), a nuclear receptor whose endogenous ligand has an aromatic A ring (estradiol). Drugs acting through the inhibition or modulation of ERs are frequently used as a hormonal therapy for ER(+) breast cancer. Previous results suggested that the aromatic D ring was a key structural motif for the observed activity; thus, this modified steroid nucleus may provide a new scaffold for the design of novel antiestrogens. Using molecular dynamics (MD) simulation we have modeled the binding mode of the natural salpichrolide A and a synthetic analog with an aromatic D ring within the ERα. These results taken together with the calculated energetic contributions associated to the different ligand‐binding modes are consistent with a preferred inverted orientation of the steroids in the ligand‐binding pocket with the aromatic ring D occupying a position similar to that observed for the A ring of estradiol. Major changes in both dynamical behavior and global positioning of H11 caused by the loss of the ligand–His524 interaction might explain, at least in part, the molecular basis of the antagonism exhibited by these compounds. Using steered MD we also found a putative unbinding pathway for the steroidal ligands through a cavity formed by residues in H3, H7, and H11, which requires only minor changes in the overall receptor conformation. Proteins 2015; 83:1297–1306. © 2015 Wiley Periodicals, Inc.     

Partial purification and characterization of UDPG:t-cinnamate glucosyltransferase in the root of sweet potato, Ipomoea batatas Lam

Previously, we isolated t-cinnamoyl-D-glucose as a possible intermediate in chlorogenic acid biosynthesis from sweet potato root. The enzyme which catalyzes the formation of t-cinnamoyl-D-glucose has been purified 539-fold from sweet potato root (Ipomoea batatas Lam.) and characterized. It required UDP-glucose as a glucosyl donor. Its molecular weight was estimated to be 45,000 by gel filtration chromatography through Sephadex G-100. Its Km values were 0.2 mM for t-cinnamic acid and 0.1 mM for UDP-glucose. It also showed activity toward various aromatic carboxylic acids other than t-cinnamic acid with the following relative activities at the concentration of 1.8 mM: t-cinnamic acid, 100; p-coumaric acid, 57; o-coumaric acid, 52; caffeic acid, 15; benzoic acid, 71; ferulic acid, 27; 4-hydroxyl-3-methoxy-benzoic acid, 35. When p-coumaric acid was used as a substrate, the enzyme introduced the glucosyl group exclusively to a carboxyl group, not to a hydroxyl group on a benzene ring. It was inhibited by p-chloromercuribenzoate and HgCl2. Its activity in the extract from sliced root decreased during the first 28 h after slicing, then increased to the original level by 75 h. The apparent decrease seemed to be caused by the appearance of an inhibitory factor of high molecular weight in the tissue extract.     

Degradation of phenanthrene by the rhizobacterium Ensifer meliloti

The biodegradation of the polycyclic aromatic hydrocarbon phenantherene by the rhizobacterial strain Ensifer meliloti P221, isolated from the root zone of plant grown in PAH-contaminated soil was studied. Bacterial growth and phenanthrene degradation under the influence of root-exuded organic acids were also investigated. Analysis of the metabolites produced by the strain by using thin-layer chromatography, gas chromatography, high-pressure liquid chromatography, and mass-spectrometry revealed that phenanthrene is bioconverted via two parallel pathways. The first, major pathway is through terminal aromatic ring cleavage (presumably at the C3–C4 bond) producing benzocoumarin and 1-hydroxy-2-naphthoic acid, whose further degradation with the formation of salicylic acid is difficult or is very slow. The second pathway is through the oxidation of the central aromatic ring at the C9–C10 bond, producing 9,10-dihydro-9,10-dihydroxyphenanthrene, 9,10-phenanthrenequinone, and 2,2′-diphenic acid. This is the first time that the dioxygenation of phenanthrene at the C9 and C10 atoms, proven by identification of characteristic metabolites, has been reported for a bacterium of the Ensifer genus.     

Redox-active dinitrodiphenylthioethers against Leishmania: Synthesis,structure–activity relationships and mechanism of action studies

BTB 06237 (2-[(2,4-dichloro-5-methylphenyl)sulfanyl]-1,3-dinitro-5-(trifluoromethyl) benzene), a compound previously identified through QSAR pharmacophore development and a virtual screen of the Maybridge database, possesses potent and selective activity against Leishmania parasites. In the present study, several analogs of BTB 06237 were synthesized and analyzed for activity against Leishmania axenic amastigotes, their ability to reduce the level of parasitemia in peritoneal macrophages, and their ability to generate reactive oxygen species (ROS) in L. donovani promastigotes. It was found that an aromatic ring must be present in the position occupied by the 2,4-dichloro-5-methylphenyl group in the lead compound, but changing the functional groups generally has little effect on the antileishmanial potency. Alterations to the 1,3-dinitro-5-(trifluoromethyl)benzene ring have more influence on antiparasitic activity with two aromatic nitro groups and a third electron-withdrawing group being required. This structural requirement corresponds with redox potential, the ability to generate ROS in the parasites, and dissipation of the mitochondrial membrane potential. Finally, we used this collection of data to design a new antileishmanial compound with strong activity in vitro and improved properties as an antileishmanial candidate.     

The molecular basis of the antidepressant action of the magic mushroom extract,psilocin

Magic mushrooms, and their extract psilocybin, are well-known for their psychedelic properties and recreational use. Psilocin, the bio-active form of psilocybin, can potentially treat various psychiatric diseases. Psilocin putatively exerts its psychedelic effect as an agonist to the serotonin 2A receptor (5-HT_2AR), which is also the receptor for the neurological hormone serotonin. The two key chemical differences between the two molecules are first, that the primary amine in serotonin is replaced with a tertiary amine in psilocin, and second, the hydroxyl group is substituted differently on the aromatic ring. Here, we find that psilocin can bind to 5-HT_2AR with an affinity higher than serotonin, and provide the molecular logic behind the higher binding affinity of psilocin using extensive molecular dynamics simulations and free energy calculations. The binding free energy of psilocin is dependent upon the protonation states of the ligands, as well as that of the key residue in the binding site: Aspartate 155. We find that the tertiary amine of psilocin, and not the altered substitution of the hydroxyl group in the ring is responsible for the increased affinity of psilocin. We propose design rules for effective antidepressants based on molecular insights from our simulations.     

Mechanism of specific inhibition of phototropism by phenylacetic Acid in corn seedling

Using geotropism as a control for phototropism, compounds similar to phenylacetic acid that photoreact with flavins and/or have auxin-like activity were examined for their ability to specifically inhibit phototropism in corn seedlings using geotropism as a control. Results using indole-3-acetic acid, napthalene-1-acetic acid, naphthalene-2-acetic acid, phenylacetic acid, and β-phenylpyruvic acid suggest that such compounds will specifically inhibit phototropism primarily because of their photoreactivity with flavins and not their auxin activity. For example, strong auxins, indole-3-acetic acid and naphthalene-1-acetic acid, affected both tropic responses at all concentrations tested whereas weak auxins, phenylacetic acid and naphthalene-2-acetic acid, exhibited specific inhibition. In addition, the in vivo concentration of phenylacetic acid required to induce specificity was well below that required to stimulate coleoptile growth. Estimates of the percentage of photoreceptor pigment inactivated by phenylacetic acid (>10%) suggest that phenylacetic acid could be used to photoaffinity label the flavoprotein involved in corn seedling phototropism.     

Epoxide Formation on the Aromatic B Ring of Flavanone by Biphenyl Dioxygenase of Pseudomonas pseudoalcaligenes KF707

Prokaryotic dioxygenase is known to catalyze aromatic compounds into their corresponding cis-dihydrodiols without the formation of an epoxide intermediate. Biphenyl dioxygenase from Pseudomonas pseudoalcaligenes KF707 showed novel monooxygenase activity by converting 2(R)- and 2(S)-flavanone to their corresponding epoxides (2-(7-oxabicyclo[4.1.0]hepta-2,4-dien-2-yl)-2, 3-dihydro-4H-chromen-4-one), whereby the epoxide bond was formed between C2′ and C3′ on the B ring of the flavanone. The enzyme also converted 6-hydroxyflavanone and 7-hydroxyflavanone, which do not contain a hydroxyl group on the B-ring, to their corresponding epoxides. In a previous report (S.-Y. Kim, J. Jung, Y. Lim, J.-H. Ahn, S.-I. Kim, and H.-G. Hur, Antonie Leeuwenhoek 84:261-268, 2003), however, we found that the same enzyme showed dioxygenase activity toward flavone, resulting in the production of flavone cis-2′,3′-dihydrodiol. Extensive structural identification of the metabolites of flavanone by using high-pressure liquid chromatography, liquid chromatography/mass spectrometry, and nuclear magnetic resonance confirmed the presence of an epoxide functional group on the metabolites. Epoxide formation as the initial activation step of aromatic compounds by oxygenases has been reported to occur only by eukaryotic monooxygenases. To the best of our knowledge, biphenyl dioxygenase from P. pseudoalcaligenes KF707 is the first prokaryotic enzyme detected that can produce an epoxide derivative on the aromatic ring structure of flavanone.     

Action of Plant Growth Regulators. IV. Adsorption of Unsubstituted and 2,6-Dichloro-aromatic Acids to Oat Monolayers

The adsorption of chloro-aromatic acids to monomolecular layers of oat squashes is reported in earlier papers but it was not possible by the technique used, to measure unambiguously the adsorption of unsubstituted and 2,6-dichloro-aromatic acids. This has now been achieved by a modification of the earlier method and involves assessments of competitive adsorption between the unknown acid and a standard acid, using measurements of surface potential.

Benzoic and phenoxyacetic acids were not adsorbed but phenylacetic acid was weakly adsorbed. The second ring in naphthalene and naphthoxyacetic acids greatly increased adsorption. Substitution of the 2 and 6 positions in the phenyl and phenoxyacetic acids resulted in low adsorption but 2,6-disubstituted phenoxybutyric and benzoic acids were more highly adsorbed.

The adsorption values from earlier work are combined and discussed in relation to the growth-regulating activity of the acids. It is conciuded that there is no direct relation embracing all acids between adsorption and activity, notable exceptions being those substituted by chlorine in the 3-position of the aromatic ring. However, for a number of acids it is suggested that activity is limited not only by their ability to interact at enzyme sites but also by the amount of acid immobilised by adsorption when moving to these sites. It is also concluded that the hydrophilic/lipophilic balance of a growth regulator sometimes used as a guide to its activity, is an unreliable indication of interfacial behaviour.

     

Root geotropism and the role of growth regulators from the cap: a re-examination

Abstract. It is widely believed that the root cap participates in geotropism by acting both as a sensor of the direction of gravity and as a source of at least one regulator of root growth, which may be abscisic acid (ABA). It has been suggested that this regulator accumulates within the prospective concave (or lower) half of the root and there causes a retardation of growth that brings about bending. A re-examination of the evidence upon which this inhibitor hypothesis of geotropic control is based reveals that (1) it is derived almost entirely from microsurgical studies and the deductions from such experiments still require corro-orations from analyses of inhibitor content and action; (2) the evidence that ABA is the inhibitor seems poor at present; (3) in maize and lentil, two well-studied species, geocurvature is probably a consequence of accelerated growth within the prospective convex (or upper) half rather than inhibited growth within the concave (or lower) half; (4) the geotropic signal from the cap may be one that redirects a pre-existing basipetal flow of inhibitor away from the upper     

Abscisic acid levels in the root tips of seven Zea mays varieties

Seven varieties of Zea mays were analysed for cis-abscisic acid (ABA) and trans-ABA levels in the primary root tips by a stable isotope dilution technique. Differences in ABA levels were observed between the first 1 mm apical segments of the different varieties. No trans-ABA could be detected. In the next 2 mm ofthe root segments, the amount of ABA did not vary very much from one variety to another. The levels of ABA might very well reflect the growth reactivity of the root tips towards geotropism and light.     

CD4 mimics as HIV entry inhibitors: Lead optimization studies of the aromatic substituents

Several CD4 mimics have been reported as HIV-1 entry inhibitors that can intervene in the interaction between a viral envelope glycoprotein gp120 and a cell surface protein CD4. Our previous SAR studies led to a finding of a highly potent analogue 3 with bulky hydrophobic groups on a piperidine moiety. In the present study, the aromatic ring of 3 was modified systematically in an attempt to improve its antiviral activity and CD4 mimicry which induces the conformational changes in gp120 that can render the envelope more sensitive to neutralizing antibodies. Biological assays of the synthetic compounds revealed that the introduction of a fluorine group as a meta-substituent of the aromatic ring caused an increase of anti-HIV activity and an enhancement of a CD4 mimicry, and led to a novel compound 13a that showed twice as potent anti-HIV activity compared to 3 and a substantial increase in a CD4 mimicry even at lower concentrations.     

Flexibility of small molecular CD4 mimics as HIV entry inhibitors

CD4 mimics such as YIR-821 and its derivatives are small molecules which inhibit the interaction between the Phe43 cavity of HIV-1 gp120 with host CD4, an interaction that is involved in the entry of HIV to cells. Known CD4 mimics generally possess three structural features, an aromatic ring, an oxalamide linker and a piperidine moiety. We have shown previously that introduction of a cyclohexyl group and a guanidine group into the piperidine moiety and a fluorine atom at the meta-position of the aromatic ring leads to a significant increase in the anti-HIV activity. In the current study, the effects of conformational flexibility were investigated by introduction of an indole-type group in the junction between the oxalamide linker and the aromatic moiety or by replacement of the oxalamide linker with a glycine linker. This led to the development of compounds with high anti-HIV activity, showing the importance of the junction region for the expression of high anti-HIV activity. The present data are expected to be useful in the future design of novel CD4 mimic molecules.     

Auxin Transport Inhibitors: III. Chemical Requirements of a Class of Auxin Transport Inhibitors

The structural requirements of a proposed class of auxin transport inhibitors have been shown to be very similar to those required to inhibit the cress (Lepidium sativum) root geotropic response. A 2-carboxyphenyl group separated by a conjugated system of atoms from a second aromatic ring appears to be necessary for a molecule to have high activity.     

Increased disease resistance and enzyme activity induced by ethylene and ethylene production of black rot infected sweet potato tissue

Exposure of root tissue from a susceptible variety of sweet potato to low concentrations of ethylene induced a resistance to infection by Ceratocystis fimbriata and an increase in the activity of peroxidase and polyphenoloxidase in the tissue. Susceptible tissue that was inoculated with a pathogenic strain of C. fimbriata or a nonpathogenic strain that can induce resistance liberated more ethylene into closed chambers than tissue inoculated with strains that did not induce resistance. It is suggested that ethylene may be a stimulus that diffuses from infected areas into adjoining tissue to initiate metabolic changes which may lead to disease resistance. Polyphenol oxidase but not peroxidase activity was increased in slices of potato tubers and parsnip roots treated with ethylene. The activity of these enzymes in root tissue of carrot, radish or turnip was not altered by ethylene treatment.     

ON REVERSAL OF GEOTROPISM IN ASTERINA

A certain level of strychninization induces in Asterina reversal of geotropism from the normally geonegative movement to a persistent downward creeping. The effect of an attached float producing upward pull is to induce upward creeping, under these conditions, whereas normally it leads to downward movement. This reversal cannot be regarded as due to a mere intensification of the sensory effect of tension. It must be understood as representing a true reversal of inhibition. The temporary reversal of geotropism following mechanical disturbances (in the absence of strychnine) is interpreted in the same way.     

A Structure-Activity Study with Aryl Acylamidases

We examined the relationship between chemical structure and biodegradability of acylanilide herbicides by using a set of model compounds. Four bacterial isolates (one gram-negative and three gram-positive) that grew on acetanilide were used. These soil isolates cleaved the amide bond of acetanilide via an aryl acylamidase reaction, producing aniline and the organic acid acetate. A series of acetanilide analogs with alkyl substitutions on the nitrogen atom or the aromatic ring were tested for their ability to induce aryl acylamidase activity and act as substrates for the enzyme. The substrate range, in general, was limited to those analogs not disubstituted in the ortho position of the benzene ring or which did not contain an alkyl group on the nitrogen atom. These same N-substituted compounds did not induce enzyme activity either, whereas the ortho-substituted compounds could in some cases.