Structure-Plant Phytotoxic Activity Relationship of 7,7′-epoxylignanes, (+)- and (−)-verrucosin: Simplification on the aromatic ring substituents

The synthesized 7-aryl derivatives of (7R,7′S,8S,8′S)-(+)-verrucosin were applied to growth inhibitory activity test against ryegrass at 1 mM. 7-(3-Ethoxy-4-hydroxyphenyl) derivative 12 and 7-(2-hydroxyphenyl) derivative 4 showed comparable activity to those of (+)-verrucosin against the root (−95%) and the shoot (−60%), respectively. The growth inhibitory activity test against lettuce using synthesized 7-aryl derivatives of (7S,7′R,8R,8′R)-(−)-verrucosin at 1 mM showed that the activities of 7-(3-hydroxyphenyl) derivative 20 and 7-(3-ethoxy-4-hydroxyphenyl) derivative 28 are similar to that of (−)-verrucosin against the root (−95%). Against the shoot, 7-(3-hydroxyphenyl) derivative 20 showed higher activity (−80%) than that of (−)-verrucosin (−60%). As the next step, (7S,7′R,8R,8′R)-7-(3-hydroxyphenyl)-7′-aryl-(−)-verrucosin derivatives, in which the most effective 3-hydroxyphenyl group is employed as 7-aromatic ring, were synthesized for the assay against lettuce. In this experiment, 7′-(2-hydroxyphenyl) derivative 37 and 7′-(3-hydroxyphenyl) derivative 38 showed similar activity to that of derivative 20. The effect of 7- and 7′-aryl structures of 7,7′-epoxylignanes on the plant growth inhibitory activity was clarified. The 7- and 7′-aryl structures were simplified to show comparable activity to or higher activity than that of (−)-verrucosin. The plant growth inhibitory activity of a nutmeg component, (+)-fragransin C_3b, was estimated as −80% inhibition at 1 mM against ryegrass roots.     

Synthesis,Antioxidant Activity,and Structure–Activity Relationship of SCAP1 Analogues

Nine analogues of antioxidant peptide SCAP1 were successfully synthesised using a solid-phase method on a 2-chlorotrytil resin. The compounds were obtained in a range of yields of 7.0–57.8%. The occurrence of aggregation during the synthesis is suspected to be responsible for the poor yields. All peptides were characterized by high-resolution time-of-flight mass spectrometry (HR-TOFMS) and nuclear magnetic resonance (NMR). The antioxidant activities of the SCAP1 analogues as well as SCAP1 were analysed utilising the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) assay. The results revealed that all of the analysed peptides exhibited moderate antioxidant properties. Moreover, the evaluation of the structure–activity relationship showed that the Asn residue is an important requirement for the antioxidant activity of SCAP1. The replacement of Asn with other amino acid residues (Thr, Pro, Tyr, Trp and Phe) resulted in a decrease in the IC₅₀ values of the peptides. Notably, however, the replacement of the Lys residue with Val marginally increased the activity.

     

Chromone-Fused Cytosine Analogues: Synthesis,Biological Activity,and Structure–Activity Relationship

The preparation of a series of novel chromone-fused cytosine analogues, i.e., chromeno[2,3-d]pyrimidines has been carried out from substituted 2-amino-4-oxo-4H-chromene-3-carbonitriles with urea, thiourea, and guanidine under different reaction conditions. These chromone-fused cytosine analogues were evaluated for their in vitro activity against Mycobacterium tuberculosis H₃₇Rv strain and different microbial pathogenic strains in cell culture for their structure–activity relationships, respectively. Among the synthesized compounds, 2d, 3a, and 4e showed better results against Mycobacterium tuberculosis H₃₇Rv. The compounds 2a, 2b, and 3a showed potential antibacterial activity against E. coli and P. aeruginosa, while the majority of compounds were found to be active against S. aureus as compared to ampicillin. The synthesized cytosine analogues having an imine (–C&dbnd;NH) have been less sensitive to the bacterial and fungal strains but have a more beneficial effect on Mycobacterium tuberculosis H₃₇Rv.     

Anti-Hiv-1 Activity of 2′,3′-Dideoxinucleoside Analogues : Structure-Activity Relationship

Abstract

Among the purine and pyrimidine 2′,3′-dideoxynucleosides, 2′,3′-didehydro-2′,3′-dideoxynucleosides, 3′-azido-2′,3′-dideoxynucleosides and 3′-fluoro-2′,3′-dideoxynucleosides, several congeners have been identified which achieve a potent and selective inhibition of HIV-1 replication in vitro.     

Structure-Herbicidal Activity Relationship of α-Phenylsulfonyl Propanamide

α-Phenylsulfonyl alkanamides were synthesized, and their herbicidal activities were tested under paddy conditions. Some of the α-phenylsulfonyl propanamides showed a high herbicidal activity against paddy weeds with no significant effect on rice plants. The activity of the sulfonyl compound was superior to those of the sulfinyl and thio compounds.     

Relationship Between Conformation and Antiviral Activity -IV. 5-Ethyl-2′-Deoxyurldine and 5-Ethyl-2′-Deoxycytidine +

Abstract

5-Ethyl-2′-deoxyuridine(EtdUrd), though a potent inhibitor of herpes simplex virus (HSV) replication, is rapidly catabolized to produce an inactive pyrimidine base by thymidine and/or uridine phosphorylases. 5-Ethyl-2′-deoxycytidine (EtdCyd) was synthesized to confer metabolic stability and thus improve efficacy against systemic HSV infections. EtdCyd was inactive against HSV in the presence or absence of deaminase inhibitors in VERO cells up to 2 mM. The relationship between molecular conformation and antiherpes activity for EtdUrd and EtdCyd is discussed.

     

Antifungal Activity of Tetra-Substituted Tetrahydrofuran Lignan, (−)-Virgatusin,and Its Structure-Activity Relationship

Antifungal activities of the optically pure (>99%ee) (?)- and (+)-virgatusin, a tetra-substituted tetrahydrofuran lignan, were tested. (?)-Virgatusin, which is a natural product, showed highest antifungal activity against Colletotrichum lagenarium. Research on its structure-activity relationship was also performed. It was shown that two methoxy groups on 9 and 9′ positions and a 3,4-methylenedioxyphenyl group on the 7 position of virgatusin were essential for high fungal growth inhibition. The part on 7′-phenyl group was not essential for activity. The 7′-(4-methoxyphenyl) derivative showed higher activity than that of (?)-virgatusin.     

3′-Phosphoadenosine-5′-Phosphate Phosphatase Activity Is Required for Superoxide Stress Tolerance in Streptococcus mutans

Aerobic microorganisms have evolved different strategies to withstand environmental oxidative stresses generated by various reactive oxygen species (ROS). For the facultative anaerobic human oral pathogen Streptococcus mutans, the mechanisms used to protect against ROS are not fully understood, since it does not possess catalase, an enzyme that degrades hydrogen peroxide. In order to elucidate the genes that are essential for superoxide stress response, methyl viologen (MV)-sensitive mutants of S. mutans were generated via ISS1 mutagenesis. Screening of approximately 2,500 mutants revealed six MV-sensitive mutants, each containing an insertion in one of five genes, including a highly conserved hypothetical gene, SMU.1297. Sequence analysis suggests that SMU.1297 encodes a hypothetical protein with a high degree of homology to the Bacillus subtilis YtqI protein, which possesses an oligoribonuclease activity that cleaves nano-RNAs and a phosphatase activity that degrades 3′-phosphoadenosine-5′-phosphate (pAp) and 3′-phosphoadenosine-5′-phosphosulfate (pApS) to produce AMP; the latter activity is similar to the activity of the Escherichia coli CysQ protein, which is required for sulfur assimilation. SMU.1297 was deleted using a markerless Cre-loxP-based strategy; the SMU.1297 deletion mutant was just as sensitive to MV as the ISS1 insertion mutant. Complementation of the deletion mutant with wild-type SMU.1297, in trans, restored the parental phenotype. Biochemical analyses with purified SMU.1297 protein demonstrated that it has pAp phosphatase activity similar to that of YtqI but apparently lacks an oligoribonuclease activity. The ability of SMU.1297 to dephosphorylate pApS in vivo was confirmed by complementation of an E. coli cysQ mutant with SMU.1297 in trans. Thus, our results suggest that SMU.1297 is involved in superoxide stress tolerance in S. mutans. Furthermore, the distribution of homologs of SMU.1297 in streptococci indicates that this protein is essential for superoxide stress tolerance in these organisms.Streptococcus mutans, a gram-positive bacterium with a low G+C content, is widely considered the primary etiological agent of dental caries, a common human infectious disease (16, 23). S. mutans is also an important agent of infective endocarditis, as a large number of cases of viridans streptococcus-induced endocarditis are caused by S. mutans (18). During colonization of the oral cavity, S. mutans encounters various environmental stresses, including nutritional limitation, temperature fluctuation, osmotic shock, low pH conditions, radiation, toxins, and variations in oxygen tension (21). Despite these harsh conditions, S. mutans has developed multiple mechanisms for successful survival in the human host by forming diverse and densely populated biofilms on the tooth surface (4). The extraordinary ability of S. mutans to adapt and flourish in the diverse and adverse environment of the oral cavity emphasizes the fundamental importance of the need for detailed analyses of the molecular mechanisms of stress tolerance response in this organism.S. mutans is a facultative anaerobic organism, but it can tolerate aerobic conditions for colonization and survival. Like other streptococci, it does not possess cytochromes and therefore cannot carry out energy-conserving oxidative phosphorylation (2). However, irrespective of the growth conditions, S. mutans derives the energy for growth through fermentation of glucose and other sugars (26). This can lead to unwanted consequences, especially when the organism is exposed to aerobic conditions in the oral cavity. If the molecular oxygen is not fully reduced by the four-electron reduction step to water, it can undergo one- or two-electron reductions to form reactive superoxide radicals, hydroxyl radicals, and hydrogen peroxide, collectively known as reactive oxygen species (ROS) (19). These radicals, when accumulated in large amounts, can trigger oxidation of lipid, protein, and nucleic acid inside the cell, ultimately leading to cellular death (19, 20).Aerobic bacteria have developed multiple strategies to adapt and protect against ROS insults (19). These strategies include (i) enzymes that scavenge ROS, such as superoxide dismutases (SOD), catalases, and peroxidases; (ii) protein repair systems, such as thioredoxin; (iii) DNA damage repair enzymes such as RecA; and (iv) proteins that regulate intracellular iron level to ameliorate the generation of ROS. Although streptococci contain SOD, NADH oxidase, glutathione reductase, and other proteins to counter ROS threats, they do not contain catalase, a key protective enzyme against oxidative radicals. Therefore, the defense strategy against damage by ROS is significantly different in streptococci than in other bacteria. For example, the growth of S. mutans in planktonic or biofilm mode can influence the respiratory rates as well as the activities of the protective enzymes, such as SOD and NADH oxidase (31).Apart from studies related to the physiology of oxidative stress in S. mutans, very little information is available on the oxidative-stress response and its regulation in this organism. Many key regulatory genes, including members of the OxyR and SoxR families, which are involved in sensing and responding to ROS attacks, are not encoded in the genome of S. mutans (2). Instead, S. mutans has a PerR homolog, which has been shown to be involved in hydrogen peroxide stress response in this organism (21). The luxS gene of S. mutans, which encodes an enzyme that synthesizes the intercellular signaling molecule AI-2, is also involved in the oxidative-stress response (52). However, the exact mechanism by which LuxS participates in the oxidative-stress response is currently unknown. Furthermore, a recent investigation suggests that a two-component signal transduction system, ScnRK, is necessary for counteracting ROS in S. mutans (11).The major focus of this study was to identify the genes that are involved in the defense against superoxide stress of S. mutans strain UA159. Toward this end, a library of mutants was generated by insertion mutagenesis, and the mutants were screened for their sensitivity to methyl viologen (MV), a superoxide-generating compound. This study enabled the identification of five loci that are potentially involved in superoxide tolerance. One of the identified loci is SMU.1297, which encodes a protein homologous to YtqI of Bacillus subtilis. The biochemical characterization of SMU.1297 and its role in superoxide stress tolerance response are presented.     

Thermodynamic and Kinetic Characterization of Duplex Formation between 2′-O, 4′-C-Methylene-modified Oligoribonucleotides,DNA and RNA

2′-O,4′-C-methylene-linked ribonucleotide derivatives, named LNA (locked nucleic acid) and BNA (bridged nucleic acid) are nucleic acid analogoues that have shown high-affinity recognition of DNA and RNA, and the employment of LNA oligomers for antisense activity, gene regulation and nucleic acid diagnostics seems promising. Here we show kinetic and thermodynamic results on the interaction of a series of 10 bases long LNA–DNA mixmers, gabmers as well as full length LNA’s with the complementary DNA, RNA and LNA oligonucleotides in the presence and absence of 10 mM Mg²⁺- ions. Our results show no significant differences in the reaction thermodynamics and kinetics between the LNA species, only a tendency to stronger duplex formation with the gabmer and mixmer. Introduction of a few LNA’s thus may be a better strategy, than using full length LNA’s to obtain an oligonucleotide that markedly increases the strength of duplexes formed with the complementary DNA and RNA.     

Structure–Depolarizing Activity Relationship for Achatin-I,a Tetrapeptide with a d-Phe Residue,and Its Derivatives toward the Crayfish Giant Axon

Achatin-I (Gly-d-Phe-Ala-Asp) is a tetrapeptide isolated from the ganglia of an African giant snail (Achatina fulica Férussac). The compound and its derivatives were synthesized, and their effects on the action potential of the crayfish giant axon elicited by electrical stimulation were examined by an intracellular recording method. The membrane potential after the action potential had fallen was elevated by some compounds at an acidic but not neutral pH level. An analysis of the structure-activity relationship for the activity to elevate the afterpotential at an acidic pH level, suggests that the factors favorable for activity were the β-turn conformation, a β- or γ-carboxyl group in the C-terminal residue, appropriate hydrophobicity and/or bulkiness in the protecting groups for the α-amino group at the N-terminus, and the number of negative charges in the entire molecule.     

2′-Fluoro-4′-thio-2′,3′-unsaturated Nucleosides: Anti-HIV Activity,Resistance Profile,and Molecular Modeling Studies

Abstract

Both D- and L-2′-fluoro-4′-thio-2′,3′-unsaturated nucleosides were synthesized and their anti-HIV activity against the drug sensitive virus and lamivudine-resistant mutant (M184V) were evaluated. In vitro antiviral evaluation indicated that the L-isomers are more potent than the D-isomers, but unfortunately all were cross-resistant with 3TC. Molecular modeling studies revealed that the unnatural sugar moiety of the L-nucleosides as well as 4′-sulfur atom of the D-isomer has a steric conflict with the bulky side chain of valine 184, resulting in cross-resistance.     

Synthesis,Cytostatic Activity and Inhibition of Ribonucleotide Reductase by 5′-Phosphoramidates and 5′-Diphosphates,of 2′-O-Allyl-arabinofuranosyl Nucleosides

Abstract

The diphosphates of a series of 2′-O-allyl-1-β-D-arabinofuranosyl derivatives, previously obtained by us, have been prepared and tested for their inhibitory activity in an in vitro assay using R1 and R2 subunits of the purified recombinant mouse ribonucleotide reductase (RNR). 2′-O-Allyl-araU diphosphate proved to be inhibitory, with an IC₅₀ of 100 μM. The 5′-phosphoramidate pronucleotide of 2′-O-allyl-araU was also prepared and tested for inhibition of tumor cell proliferation.     

Benzimidazole 2′-Isonucleosides: Design,Synthesis, and Antiviral Activity of 2-Substituted-5,6-Dichlorobenzimidazole 2′-Isonucleosides

Abstract

2,5,6-Trihalogenated benzimidazole-β-D-ribofuranosyl nucleosides and 2-substituted amino-5,6-dichlorobenzimidazole-β-L-ribofuranosyl nucleosides are potent and selective inhibitors of human cytomegalovirus (HCMV). The D-ribofuranosyl analogs are metabolized rapidly in vivo rendering them unsuitable as drug candidates. The primary source of instability is thought to be the anomeric bond. The synthesis of a series of chemically stable benzimidazole-2′-isonucleosides is presented. The synthetic schemes employed are based on nucleophilic displacements of a 2′-tosylate from carbohydrate intermediates with 2-bromo-5,6-dichlorobenzidazole. 2-Bromo and 2-isopropyl amino analogs with 3′- and 5′-oxo and deoxy substitutions were prepared. The benzimidazole-2′-isonucleosides presented here demonstrated reduced activity against HCMV when compared to other D-ribofuranosyl benzimidazole analogs. In addition, they were not found to be inhibitors of HIV.     

Structure–Activity Relationship of novel phenylacetic CXCR1 inhibitors

We reported recently the Structure–Activity Relationship (SAR) of a class of CXCL8 allosteric modulators. They invariably share a 2-arylpropionic moiety so far considered a key structural determinant of the biological activity. We show the results of recent SAR studies on a novel series of phenylacetic derivatives supported by a combined approach of mutagenesis experiments and conformational analysis. The results suggest novel insights on the fine role of the propionic/acetic chain in the modulation of CXCL8 receptors.     

Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3′-O, 5′-S) thymidine phosphodiester derivatives

Hydrolysis of nucleic acids is of fundamental importance in biological sciences. Kinetic and theoretical studies on different substrates wherein the phosphodiester bond combined with alkyl or aryl groups and sugar moiety have been the focus of attention in recent literature. The present work focuses on understanding the mechanism and energetics of alkali metal (Li, Na, and K) catalyzed hydrolysis of phosphodiester bond in modeled substrates including Thymidylyl (3′-O, 5′-S) thymidine phosphodiester (Tp-ST) (1), 3′-Thymidylyl (1-trifluoroethyl) phosphodiester (Tp-OCH₂CF₃) (2), 3′-Thymidylyl (o-cholorophenyl) phosphodiester (Tp-OPh(o-Cl)) (3) and 3′-Thymidylyl(p-nitrophenyl) phosphodiester (Tp-OPh(p-NO₂)) (4) employing density functional theory. Theoretical calculations reveal that the reaction follows a single-step (A_ND_N) mechanism where nucleophile attack and leaving group departure take place simultaneously. Activation barrier for potassium catalyzed Tp-ST hydrolysis (12.0 kcal mol^?1) has been nearly twice as large compared to that for hydrolysis incorporating lithium or sodium. Effect of solvent (water) on activation energies has further been analyzed by adding a water molecule to each metal ion of the substrate. It has been shown that activation barrier of phosphodiester hydrolysis correlates well with basicity of leaving group.

Refinement of a Quantitative Structure–Activity Relationship Model for Prediction of Cell-Penetrating Peptide Based Transfection Systems

Cell-penetrating peptide (CPP) based transfection systems (PBTS) are a promising class of drug delivery vectors. CPPs are short mainly cationic peptides capable of delivering cell non-permeant cargo to the interior of the cell. Some CPPs have the ability to form non-covalent complexes with oligonucleotides for gene therapy applications. In this study, we use quantitative structure–activity relationships (QSAR) , a statistical method based on regression data analysis. Here, an fragment QSAR (FQSAR) model is developed to predict new peptides based on standard alpha helical conformers and Assisted Model Building with Energy Refinement molecular mechanics simulations of previous peptides. These new peptides were examined for plasmid transfection efficiency and compared with their predicted biological activity. The best predicted peptides were capable of achieving plasmid transfection with significant improvement compared to the previous generation of peptides. Our results demonstrate that FQSAR model refinement is an efficient method for optimizing PBTS for improved biological activity.     

Synthesis and Antiviral Activity of L-2′-Deoxy-2′-up-fluoro-4′-thionucleosides

Abstract

L-2′-Deoxy-2′-up-fluoro-4′-thionucleosides were efficiently synthesized from D-xylose via L-4-thioarabitol derivative as a key intermediate and evaluated for antiviral activities against HIV-1, HSV-1,2 and HBV.     

Antibacterial Activity of 2′-Esters of Erythromycin

The effect of esterification at the 2'-position of desosamine on the antibacterial activity of erythromycin was investigated by determining the bacteriostatic and bactericidal activities of erythromycin and a number of its 2'-esters on S. aureus and relating these activities to the hydrolysis rates of the esters. These studies, together with comparison of the inhibition of protein synthesis in a cell-free system isolated from S. aureus, lead to the conclusion that 2'-esters of erythromycin are inactive until hydrolyzed. Loss of activity appears to result from inability of erythromycin esters to bind to bacterial ribosomes and thus inhibit synthesis of protein.