Ribosome-inactivating proteins from plants: more than RNA N-glycosidases?

Many plants contain proteins that are capable of inactivating ribosomes and accordingly are called ribosome-inactivating proteins or RIPs. These typical plant proteins receive a lot of attention in biological and biomedical research because of their unique biological activities toward animal and human cells. In addition, evidence is accumulating that some RIPs play a role in plant defense and hence can be exploited in plant protection. To understand the mode of action of RIPs and to optimize their medical and therapeutical applications and their use as antiviral compounds in plant protection, intensive efforts have been made to unravel the enzymatic activities of RIPs and provide a structural basis for these activities. Though marked progress has been made during the last decade, the enzymatic activity of RIPs has become a controversial issue because of the concept that RIPs possess, in addition to their classical RNA N-glycosidase and polynucleotide:adenosine glycosidase activity, other unrelated enzymatic activities. Moreover, the presumed novel enzymatic activities, especially those related to diverse nuclease activities, are believed to play an important role in various biological activities of RIPs. However, both the novel enzymatic activities and their presumed involvement in the biological activities of RIPs have been questioned because there is evidence that the activities observed are due to contaminating enzymes. We offer a critical review of the pros and cons of the putative novel enzymatic activities of RIPs. Based on the available data, it is suggested that there is little conclusive evidence in support of the presumed activities and that in the past too little attention has been given to the purity of the RIP preparation. The antiviral activity and mode of action of RIPs in plants are discussed in view of their classical and presumed novel enzymatic activities.     

Diverse catalytic activities in the alphabeta-hydrolase family of enzymes: activation of H2O, HCN, H2O2, and O2

The article describes the observation of novel catalytic activities in the alphabeta-hydrolase superfamily apparently unrelated to ester hydrolysis and unexpected biochemical observations relating to the structure and function of the serine catalytic triad in these enzymes. One common feature of these novel activities is the activation of a small diatomic molecule, but via diverse chemistry. Possible mechanisms of catalysis are discussed.     

Selective fluorescence probes for dipeptidyl peptidase activity-fibroblast activation protein and dipeptidyl peptidase IV

Development of suitable tools to assess enzyme activity directly from their complex cellular environment has a dramatic impact on understanding the functional roles of proteins as well as on the discovery of new drugs. In this study, a novel fluorescence-based chemosensor strategy for the direct readout of dipeptidase activities within intact living cells is described. Selective activity-based probes were designed to sense two important type II transmembrane serine proteases, fibroblast activation protein (FAP) and dipeptidyl peptidase IV (DPP-IV). These serine proteases have been implicated in diverse cellular activities, including blood coagulation, digestion, immune responses, wound healing, tumor growth, tumor invasion, and metastasis. Here, we validated that Ac-GPGP-2SBPO and GPGP-2SBPO probes are excellent reporters of both proteolytic activities. Furthermore, the novel probes can differentiate between FAP and DPP-IV proteolytic activities in cellular assay. Potentially, this assay platform is immediately useful for novel drug discovery.     

Synthesis and antifungal activities in vitro of novel pyrazino [2,1-a] isoquinolin derivatives

A series of novel pyrazino[2,1-a]isoquinolin compounds were designed and synthesized, and their antifungal activities in vitro were evaluated. The results showed that all of the compounds exhibited antifungal activities. Some of them exhibited stronger antifungal activities than that of lead compounds and among them compound 11b was the most potent one, which showed more potent than that of the active control fluconazole to the four of the five tested fungi. The studies presented here provide a new structural type for the development of novel antifungal agents.     

Design, synthesis and biological evaluation of novel 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid derivatives as aminopeptidase N/CD13 inhibitors

A series of novel 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid derivatives were designed, synthesized and assayed for their activities against aminopeptidase N (APN/CD13) and MMP-2. The results showed that most compounds exhibited higher inhibitory activities against APN than that of MMP-2. Within this series, compound 12h (IC(50)=6.28 ± 0.11 μM) showed similar inhibitory activities compared with Bestatin (IC(50)=5.55 ± 0.01 μM), and it could be used as novel lead compound for the future APN inhibitors development as anticancer agents.     

Antibacterial Activity and Mechanism of a Bacteriocin Derived from the Valine-Cecropin A(1–8)-Plantaricin ZJ5(1–18) Hybrid Peptide Against Escherichia coli O104

Food Biophysics - Peptide fragment hybridization is an effective method to obtain novel hybrid antimicrobial peptides with higher antibacterial activities. The novel peptide, valine-cecropin...     

Two novel cytotoxic and antimicrobial triterpenoids from Pseudolarix kaempferi.

Two novel antimicrobial and cytotoxic triterpenoids, isopseudolarifuroic acids A (1) and B (2), were isolated from the bark of Pseudolarix kaempferi. The structural elucidation of two novel compounds was carried out mainly by spectroscopic methods, and also by computer modeling. Compounds 1 and 2 exhibited significant cytotoxic activities against several tumor cell lines. Compound 1 also showed most potent antimicrobial activities against both Gram-positive and Gram-negative bacteria.     

Endoglucanase activities and growth of marine‐derived fungi isolated from the sponge Haliclona simulans

Aims: The conversion of cheap cellulosic biomass to more easily fermentable sugars requires the use of costly cellulases. We have isolated a series of marine sponge‐derived fungi and screened these for cellulolytic activity to determine the potential of this unique environmental niche as a source of novel cellulase activities. Methods and Results: Fungi were isolated from the marine sponge Haliclona simulans. Phylogenetic analysis of these and other fungi previously isolated from H. simulans showed fungi from three phyla with very few duplicate species. Cellulase activities were determined using plate‐based assays using different media and sea water concentrations while extracellular cellulase activities were determined using 3,5‐dinitrosalicylic acid (DNSA)‐based assays. Total and specific cellulase activities were determined using a range of incubation temperatures and compared to those for the cellulase overproducing mutant Hypocrea jecorina QM9414. Several of the strains assayed produced total or relative endoglucanase activities that were higher than H. jecorina, particularly at lower reaction temperatures. Conclusions: Marine sponges harbour diverse fungal species and these fungi are a good source of endoglucanase activities. Analysis of the extracellular endoglucanase activities revealed that some of the marine‐derived fungi produced high endoglucanase activities that were especially active at lower temperatures. Significance and Impact of the Study: Marine‐derived fungi associated with coastal marine sponges are a novel source of highly active endoglucanases with significant activity at low temperatures and could be a source of novel cellulase activities.     

Metagenomic gene discovery: How far have we moved into novel sequence space?

Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.     

Synthesis and acrosin inhibitory activities of substituted ethyl 5-(4-aminophenyl)-1H-pyrazole-3-carboxylate derivatives

A series of novel ethyl 5-(4-aminophenyl)-1H-pyrazole-3-carboxylate derivatives were designed and synthesized and their in vitro acrosin inhibitory activities were evaluated. Most of the compounds exhibited acrosin inhibitory activities. Among them, three compounds (5l, 5n, and 5v) were more potent than that of the control TLCK. These provide a new structural type for the development of novel contraceptive acrosin inhibitory agents.     

Novel class of cyclophosphamide prodrug: cyclophosphamide spiropiperaziniums (CPSP)

A novel class of cyclophosphamide spiropiperaziniums was synthesized and evaluated for their in vivo anti-cancer activities against S180 and H22. Most of them exhibited definite activities. Especially, compounds 8b and 8k showed good anti-cancer activities, meanwhile, 8k also showed much lower toxicity than CP. Several interesting structure-activity relationships were revealed.     

Synthesis and biological evaluation of novel human Pin1 inhibitors with benzophenone skeleton

A series of novel benzophenone derivatives were prepared and their inhibitory activities were evaluated on hPin1. Of all the synthesized compounds, the most active compound displayed inhibitory activities with an IC(50) value of 5.99 μmol/L. Preliminary structure-activity relationships were analyzed in details and the binding mode of the titled compounds was predicted using FlexX algorithm. The results of this research will shed light on further design and optimization of novel small molecule Pin1 inhibitors.     

Synthesis and activities of 9-pyrrolo-9-deoxoerythromycin a analogs

Preparation of novel 9-pyrrolo-9-deoxoerythromycin A analogs from 9-(S) and (R, erythromycylamines by the Clauson-Kass and Wasserman reactions is described. The biological activities of these novel analogs are also reported.     

Synthesis and biological evaluation of novel quinazoline-derived human Pin1 inhibitors

A series of novel 2,4-disubstituted quinazoline derivatives were prepared and their inhibitory activities on hPin1 were evaluated. Of all the synthesized compounds, eight compounds displayed inhibitory activities with IC(50) value at the level of 10(-6)mol/L. Preliminary structure-activity relationships were analyzed in details and the binding mode of the titled compounds was predicted using FlexX algorithm. The design and optimization of novel small molecule Pin1 inhibitors will be guided by the results of this report.     

Synthesis and biological evaluation of novel N-acyl substituted quinolin-2(1H)-one derivatives as potential antimicrobial agents

A series of novel N-acyl substituted quinolin-2(1H)-one derivatives were synthesized and screened in vitro for their antibacterial and antifungal activities by disc diffusion method. All the compounds exhibited moderate to good antimicrobial activities, some of these compounds displayed comparable or better antibacterial or antifungal activities against some tested strains compared to the reference drugs Streptomycin and Fluconazole.     

Ribosome-Inactivating Proteins: A Family of Plant Proteins That Do More Than Inactivate Ribosomes

Many plants contain proteins that are commonly designated as ribosome-inactivating proteins (RIPs). Based on the structure of the genes and the mature proteins a novel system is proposed to unambiguously classify all RIPs in type-1, type-2, and type-3 RIPs. In addition, the concept of one- and two-chain type-1 RIPs is introduced. After an overview of the occurrence, molecular structure, and amino acid sequences of RIPs, the formation of the mature proteins from the primary translation products of the corresponding mRNAs is elaborated in detail in a section dealing with the biosynthesis, posttranslational modifications, topogenesis, and subcellular location of the different types of RIPs. Details about the three-dimensional structure of type-1 RIPs and the A and B chains of type-2 RIPs are discussed in a separate section. Based on the data given in the previous sections, the phylogenic and molecular evolution of RIPs is critically assessed and a novel model is proposed for the molecular evolution of RIPs. Subsequently, the enzymatic activities of RIPs are critically discussed whereby special attention is given to some presumed novel activities, and a brief overview is given of the biological activities of the different types of RIPs on cells and whole organisms. By combining the data on the enzymatic activities and biological activities of RIPs, and the current knowledge of different plant physiological aspects of these proteins, the role of RIPs in plants is revisited. Thereby the attention is focussed on the role of RIPs in plant defense with the emphasis on protection against plant-eating organisms and viruses. Finally, there is a short discussion on the discovery of a novel class of enzymes called RALyases that use ribosomes damaged by RIPs as a substrate and may act cooperatively with RIPs. There is discussion regarding why the identification of this novel enzyme gives valuable clues to the origin and original function of RIPs and may be helpful to unravel the physiological role of modem RIPs.     

Isoplatensimycin: Synthesis and biological evaluation

Isoplatensimycin, a novel analog of platensimycin, was synthesized via intramolecular dipolar cycloaddition of a carbonyl ylide. Isoplatensimycin showed little activities against strains of Staphylococcus aureus, but exhibited activities against some vancomycin-resistant enteroccoci.     

Design and synthesis of 6-amino-1,4-oxazepane-3,5-dione derivatives as novel broad spectrum anticonvulsants

Based on the structural estimations of the typical anticonvulsant drugs, a series of 6-amino-1,4-oxazepane-3,5-dione derivatives, novel structures of 7-membered heterocyclic imides, which were hybridized with pharmacophores such as cyclic imide and N-CO-C-N group in their molecule were designed and synthesized. Their anticonvulsant activities were evaluated by the maximal electroshock induced seizure (MES) and subcutaneous pentylenetetrazole (PTZ) tests. Almost all the designed compounds except 1c and 1f showed comparable anticonvulsant activities in at least one of the anticonvulsant tests. Moreover, some of the tested compounds exhibited moderate anticonvulsant activities in both MES and PTZ tests. From these results, 6-amino-1,4-oxazepane-3,5-dione derivatives could be recommended as novel structures of broad spectrum anticonvulsants.     

Synthesis and antiangiogenic activity of 6-amido-2,4,5-trimethylpyridin-3-ols

We recently reported that 6-aminoalkyl-2,4,5-trimethylpyridin-3-ols, novel series of 6-aminopyridin-3-ol-based antioxidants, have high antiangiogenic activities. In pursuit of wider variety in the analogues, we here report the synthesis and antiangiogenic activities of 6-amidoalkyl-2,4,5-trimethylpyridin-3-ols, which would not be considered excellent antioxidants because of the poorer electron-donating effect of the C(6)-amido group than the corresponding C(6)-amino group. The selected 6-amido compounds showed up to several fold-higher antiangiogenic activities and up to an order of magnitude better antitumor activities in the chick embryo chorioallantoic membrane (CAM) assay than SU4312, a positive control. We also found that paracetamol, as a direct phenolic analogue of our simplest 6-amidopyridin-3-ol, showed a moderate level of antiangiogenic activity. We propose this study will offer a basis for a scaffold of novel angiogenesis inhibitors that can perturb angiogenesis-related pathologies.     

Toward a systems biology perspective on enzyme evolution

Large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. Division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. Later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. Enzymes operate in the context of complex metabolic and regulatory networks. The potential for evolution of a new enzyme depends upon the collection of enzymes in a microbe, the topology of the metabolic network, the environmental conditions, and the net effect of trade-offs between the original and novel activities of the enzyme.