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PubMed2004

Antimicrobial dihydrofolate reductase inhibitors--achievements and future options: review.

Despite all progress made in the fight against infections caused by bacteria, fungi, protozoa or viruses, there is a need for more and new active agents. Intensive efforts are currently directed against many new and attractive targets, and are hoped to result in new useful agents. The opportunities offered by some known and validated targets are, however, by far not exhausted. Dihydrofolate reductase (DHFR, EC 1.5.1.3) attracted much attention over several decades, which yielded several useful agents. There are excellent chances for new drugs in this field, and they are thought to increase by limiting the spectrum of activity. Whereas trimethoprim seems to present the optimum which can be achieved for a broad spectrum antibacterial agent, specific agents could probably be designed for well defined groups or specific organisms, such as staphylococci among the bacteria, or for a number of parasites, such as Plasmodium falciparum, the fungus Pneumocystis carinii, and several protozoa, such as Trypanosoma, Toxoplasma, and others. This would even extend to herbicides or specific plant pathogens. Achievements and current efforts directed against new DHFR-inhibitors are reviewed, considering only the most recent literature.

Anti-Infective Agents↗

PubMed2005

Overview of virus-induced airway disease.

Acute exacerbations of asthma and chronic obstructive pulmonary disease (COPD) are the major cause of morbidity, mortality, and health costs of both diseases. Currently available treatments are poorly effective in both acute treatment of and prevention of acute exacerbations. New treatments for intervention and prophylaxis are therefore required; to facilitate their development, we must understand the causes and mechanisms of exacerbations. Respiratory viral infections (2/3 rhinoviruses) precipitate 80% or more of asthma exacerbations in children, and the majority of exacerbations of asthma and COPD in adults, but mechanisms of virus-induced lower airway inflammation and of host resistance against respiratory viruses are poorly understood. Development of in vitro experimental models of virus infection has identified interferon-beta and nitric oxide as possible therapeutic targets to augment antiviral immunity, and nuclear factor-kappaB as a target for development of anti-inflammatory therapies. In vivo models could also serve to identify and validate targets and as an experimental system to test candidate molecules as they emerge into clinical studies. Studies in asthma have paved the way for development of an asthma model; a similar experimental model in COPD would accelerate development of new therapies for these common diseases with enormous burdens of illness.

Airway Obstruction↗

PubMed2006

Gene silencing through RNA interference (RNAi) in vivo: strategies based on the direct application of siRNAs.

RNA interference (RNAi) offers great potential not only for in vitro target validation, but also as a novel therapeutic strategy based on the highly specific and efficient silencing of a target gene, e.g. in tumor therapy. Since it relies on small interfering RNAs (siRNAs), which are the mediators of RNAi-induced specific mRNA degradation, a major issue is the delivery of therapeutically active siRNAs into the target tissue/target cells in vivo. For safety reasons, strategies based on (viral) vector delivery may be of only limited clinical use. The more desirable approach is to directly apply catalytically active siRNAs. This review highlights the recent knowledge on the guidelines for the selection of siRNAs which show high activity in the absence of non-specific siRNA effects. It then focuses on approaches to directly use siRNA molecules in vivo and gives a comprehensive overview of in vivo studies based on the direct application of siRNAs to induce RNAi. One promising approach is the in vivo siRNA delivery through complexation of chemically unmodified siRNAs with polyethylenimine (PEI). The anti-tumoral effects of PEI/siRNA-based targeting of tumor-relevant genes in vivo are described.

Gene Silencing↗

PubMed2004

Kanizsa subjective figures capture visual spatial attention: evidence from electrophysiological and behavioral data.

Figural binding and attention are two important processes that help to perceive the outside world. Binding is necessary to link together the different features of single objects which are represented in a distributed fashion in the brain. Attention serves to focus onto a small subset of incoming information. It is still not clear how exactly these two mechanisms operate and interact. We performed two experiments employing illusory Kanizsa figures (KFs) to investigate the temporal order of figural binding and spatial attention. In a visual search task, subjects had to detect the presence of a KF among distractor stimuli. We found only a slight increase of reaction times when increasing the number of distractors, indicating that KFs popped out and drew the perceiver's attention. In a further event-related potential (ERP) study, we used displays of the search task as non-informative cue for a subsequent target choice-reaction task. Enhanced contralateral negative amplitudes (starting at about 230 ms) over ventral occipital areas were found for cue displays which included a KF. For target stimuli, faster reaction times and enhanced ipsilateral N1 amplitudes over occipito-parietal areas were observed for validly (target presentation inside a KF) as compared to invalidly cued targets (target presentation outside a KF). Furthermore, enhanced contralateral N1 amplitudes were found for invalidly cued targets. It might be that interactions between perceptual closure processing of the ventral pathway and spatial target processing of the dorsal pathway contributed to the present result. We conclude that KFs automatically capture spatial attention when used as visual cues.

Adult↗

PubMed2006

Oncogenic BRAF is required for tumor growth and maintenance in melanoma models.

The usual paradigm for developing kinase inhibitors in oncology is to use a high-affinity proof-of-concept inhibitor with acceptable metabolic properties for key target validation experiments. This approach requires substantial medicinal chemistry and can be confounded by drug toxicity and off-target activities of the test molecule. As a better alternative, we have developed inducible short-hairpin RNA xenograft models to examine the in vivo efficacy of inhibiting oncogenic BRAF. Our results show that tumor regression resulting from BRAF suppression is inducible, reversible, and tightly regulated in these models. Analysis of regressing tumors showed the primary mechanism of action for BRAF to be increased tumor cell proliferation and survival. In a metastatic melanoma model, conditional BRAF suppression slowed systemic tumor growth as determined by in vivo bioluminescence imaging. Taken together, gain-of-function BRAF signaling is strongly associated with in vivo tumorigenicity, confirming BRAF as an important target for small-molecule and RNA interference-based therapeutics.

Animals↗

PubMed1995

Comparison of the efficacy and safety of isepamicin and amikacin in the treatment of skin and skin structure infections.

Two hundred and three patients with skin and skin structure infections were treated with isepamicin once daily or amikacin twice daily in an open, randomised, comparative multicentre trial. Patients were randomised to treatment with isepamicin or amikacin in a 2:1 ratio. Severe infections (63 patients) were treated with isepamicin 15 mg/kg once daily (n = 15) or amikacin 7.5 mg/kg twice daily (n - 18), less severe infections (140 patients) with isepamicin 8 mg/kg once daily (n = 93) or amikacin 7.5 mg/kg twice daily (n = 47). The overall clinical response rate at the end of treatment was excellent in all treatment groups (94-96% cured or improved) with no significant differences between isepamicin and amikacin in patients with either server or less severe infections. The most commonly isolated target pathogens were Pseudomonas aeruginosa, Escherichia coli, Proteus mirabilis and Staphylococcus aureus. Overall, in patients who had a valid target pathogen isolated prior to treatment and who met other evaluability criteria, bacteriological eradication was achieved in over 90% of patients; amikacin patients with severe infections had a somewhat lower eradication rate (82%). Over all infections, 4/110 (4%) patients in the isepamicin group and 5/54 (9%) patients in the amikacin had organisms which persisted. Adverse events were reported in 12% of patients in the isepamicin group and 6% in the amikacin group. The most frequently reported adverse event in the isepamicin group as headache. Two patients (one in each treatment group), both of whom experienced skin rashes, were withdrawn. Potentially clinically significant changes in serum creatinine occurred in two patients, who received isepamicin and one who received amikacin (who was withdrawn from the study). Ototoxicity was rare, occurring in one patient treated with isepamicin.

Adolescent↗

PubMed2006

Proteomics-based validation of genomic data: applications in colorectal cancer diagnosis.

Multiple factors are involved in the translation of functional genomic results into proteins for proteome research and target validation on tumoral tissues. In this report, genes were selected by using DNA microarrays on a panel of colorectal cancer (CRC) paired samples. A large number of up-regulated genes in colorectal cancer patients were investigated for cellular location, and those corresponding to membrane or extracellular proteins were used for a non-biased expression in Escherichia coli. We investigated different sources of cDNA clones for protein expression as well as the influence of the protein size and the different tags with respect to protein expression levels and solubility in E. coli. From 29 selected genes, 21 distinct proteins were finally expressed as soluble proteins with, at least, one different fusion protein. In addition, seven of these potential markers (ANXA3, BMP4, LCN2, SPARC, SPP1, MMP7, and MMP11) were tested for antibody production and/or validation. Six of the seven proteins (all except SPP1) were confirmed to be overexpressed in colorectal tumoral tissues by using immunoblotting and tissue microarray analysis. Although none of them could be associated to early stages of the tumor, two of them (LCN2 and MMP11) were clearly overexpressed in late Dukes' stages (B and C). This proteomic study reveals novel clues for the assembly of a robust and highly efficient high throughput system for the validation of genomic data. Moreover it illustrates the different difficulties and bottlenecks encountered for performing a quick conversion of genomic results into clinically useful proteins.

Acute-Phase Proteins↗

PubMed2026

Gravity-driven millifluidic platform for magnetic solid-phase extraction of Enterocytozoon hepatopenaei DNA from complex shrimp hepatopancreas.

Effective detection of Enterocytozoon hepatopenaei (EHP) in aquaculture is currently hindered by the lack of field-deployable extraction methods capable of processing complex, inhibitor-rich hepatopancreatic tissue. This study presents a gravity-driven millifluidic platform for the rapid extraction of EHP genomic DNA using an optimized, surfactant-compatible magnetic solid-phase extraction (MSPE) chemistry. Utilizing 5% PEG 8000 and 2.0 M NaCl, the platform facilitates the selectively capture of DNA from inhibitor-rich crustacean lysates. The 3D-printed device employs a tilting rocking plate to generate passive, gravity-driven flow, maintaining homogeneous magnetic bead suspension and maximizing solid-phase capture efficiency without external pumps. The integrated platform achieved a DNA yield of 2804.33 ± 15.31 ng/μL, a 5.9-fold increase over manual magnetic bead extraction. TaqMan quantitative PCR (qPCR) validation targeting the EHP SSU rRNA gene was developed. Using a standard curve spanning 101 to 107 plasmid copies (Ct = -3.611 log10 [copy] + 42.309, R2 = 0.998, amplification efficiency 89.2%), the on-chip MSPE achieved a validated analytical limit of detection (LOD) of 1 spore per reaction (100% detection rate, n = 21), whereas a commercial CTAB-based DNA extraction kit failed to achieve a validated LOD even at 10 spores (85.7%, 18/21). Nested PCR targeting the SWP gene was employed for field evaluation. A pilot study across two cohorts (N = 40) demonstrated consistent detection of confirmed EPH-positive cases; however, the small sample size precludes definitive diagnostic accuracy claims. With a total processing time under 30 min, this platform provides a high-efficiency extraction module. Future work will couple the device with isothermal amplification (e.g., LAMP or RPA) to realize a sample-to-answer system for resource-limited aquaculture.

Aquaculture diagnostics↗

PubMed2004

mRNA openers and closers: modulating AU-rich element-controlled mRNA stability by a molecular switch in mRNA secondary structure.

Approximately 3 000 genes are regulated in a time-, tissue-, and stimulus-dependent manner by degradation or stabilization of their mRNAs. The process is mediated by interaction of AU-rich elements (AREs) in the mRNA's 3'-untranslated regions with trans-acting factors. AU-rich element-controlled genes of fundamentally different functional relevance depend for their activation on one positive regulator, HuR. Here we present a methodology to exploit this central regulatory process for specific manipulation of AU-rich element-controlled gene expression at the mRNA level. With a combination of single-molecule spectroscopy, computational biology, and molecular and cellular biochemistry, we show that mRNA recognition by HuR is dependent on the presentation of the sequence motif NNUUNNUUU in single-stranded conformation. The presentation of the HuR binding site in the mRNA secondary structure appears to act analogously to a regulatory on/off switch that specifically controls HuR access to mRNAs in cis. Based on this finding we present a methodology for manipulating ARE mRNA levels by actuating this conformational switch specifically in a target mRNA. Computationally designed oligonucleotides (openers) enhance the NNUUNNUUU accessibility by rearranging the mRNA conformation. Thereby they increase in vitro and endogenous HuR-mRNA complex formation which leads to specific mRNA stabilization (as demonstrated for TNFalpha and IL-2, respectively). Induced HuR binding both inside and outside the AU-rich element promotes functional IL-2 mRNA stabilization. This opener-induced mRNA stabilization mimics the endogenous IL-2 response to CD28 stimulation in human primary T-cells. We therefore propose that controlled modulation of the AU-rich element conformation by mRNA openers or closers allows message stabilization or destabilization in cis to be specifically triggered. The described methodology might provide a means for studying distinct pathways in a complex cellular network at the node of mRNA stability control. It allows ARE gene expression to be potentially silenced or boosted. This will be of particular value for drug-target validation, allowing the diseased phenotype to ameliorate or deteriorate. Finally, the mRNA openers provide a rational starting point for target-specific mRNA stability assays to screen for low-molecular-weight compounds acting as inhibitors or activators of an mRNA structure rearrangement.

Antigens, Surface↗

PubMed2004

A novel mechanism for TNF-alpha regulation by p38 MAPK: involvement of NF-kappa B with implications for therapy in rheumatoid arthritis.

TNF-alpha is a key factor in a variety of inflammatory diseases. This study examines the role of p38 MAPK in the regulation of TNF-alpha in primary human cells relevant to inflammation, e.g., macrophages and rheumatoid synovial cells. Using a dominant negative variant (D168A) of p38 MAPK and a kinase inhibitor, SB203580, we confirm in primary human macrophages that p38 MAPK regulates TNF-alpha production using a posttranscriptional mechanism requiring the 3' untranslated region of the gene. However, in LPS-activated primary human macrophages we also detect a second previously unidentified mechanism, the p38 MAPK modulation of TNF-alpha transcription. This is mediated through p38 MAPK regulation of NF-kappaB. Interestingly this mechanism was not observed in rheumatoid synovial cells. Importantly however, the dominant negative mutant of p38 MAPK, but not SB203580 was effective at inhibiting spontaneous TNF-alpha production in these ex vivo rheumatoid synovial cell cultures. These data indicate there are potential major differences in the role of p38 MAPK in inflammatory signaling that have a bearing on the use of this kinase as a target for therapy. These results indicate despite disappointing results with p38 MAPK inhibitors in the clinic, this kinase is a valid target in rheumatoid disease.

3' Untranslated Regions↗

PubMed2003

Single domain intracellular antibodies: a minimal fragment for direct in vivo selection of antigen-specific intrabodies.

There is a major need in target validation and therapeutic applications for molecules that can interfere with protein function inside cells. Intracellular antibodies (intrabodies) can bind to specific targets in cells but isolation of intrabodies is currently difficult. Intrabodies are normally single chain Fv fragments comprising variable domains of the immunoglobulin heavy (VH) and light chains (VL). We now demonstrate that single VH domains have excellent intracellular properties of solubility, stability and expression within the cells of higher organisms and can exhibit specific antigen recognition in vivo. We have used this intracellular single variable domain (IDab) format, based on a previously characterised intrabody consensus scaffold, to generate diverse intrabody libraries for direct in vivo screening. IDabs were isolated using two distinct antigens and affinities of isolated IDabs ranged between 20 nM and 200 nM. Moreover, IDabs selected for binding to the RAS protein could inhibit RAS-dependent oncogenic transformation of NIH3T3 cells. The IDab format is therefore ideal for in vivo intrabody use. This approach to intrabodies obviates the need for phage antibody libraries, avoids the requirement for production of antigen in vitro and allows for direct selection of intrabodies in vivo.

3T3 Cells↗

PubMed1999

The structure-based design of ATP-site directed protein kinase inhibitors.

The protein kinase family represents both a huge opportunity and a challenge for drug development. The conservation of structural features within the ATP binding cleft initially led to the belief that specificity would be difficult to achieve. This dogma has now been clearly dispelled with the discovery and clinical testing of a group of first generation compounds, which are characterized by a high degree of selectivity towards a variety of oncology targets. The structural basis for selectivity and potency has now been clarified with the crystallization of a number of such targets in complex with inhibitors. The protein kinase inhibitor field is now ripe for the structure based exploitation of additional highly validated targets from a variety of therapeutic areas.

Adenosine Triphosphate↗

PubMed2005

Small interfering RNA for experimental cancer therapy.

RNA interference describes the recently discovered process of sequence-specific, post-transcriptional gene silencing that is initiated by double-stranded RNA molecules known as small interfering RNAs (siRNAs). siRNAs have an acceptable half-life in vitro, a predictable biodistribution profile similar to that of single-stranded antisense oligonucleotides (ASOs), and have repeatedly been more robust than ASO techniques in terms of consistency of transcript knockdown and threshold concentration. Following validation in mammalian cells by Tuschl and co-workers in 2001, synthetic siRNAs have gained wide acceptance as a laboratory tool for target validation. Currently, there is considerable interest in the therapeutic use of siRNA, particularly in areas of infectious disease and cancer. In vitro and in vivo findings demonstrate the efficacy of siRNA knockdown of gene messages that are pivotal for tumor cell growth, metastasis, angiogenesis and chemoresistance, leading to tumor growth suppression. However, siRNA-based cancer therapy faces similar pharmacokinetic limitations to ASO therapy with respect to the extent that siRNA accesses primary and metastatic target cells. The recently identified 'off-target activity' of siRNAs is also of concern. The concept of carrier-restricted delivery of siRNA by conditionally replicative, oncolytic adenoviruses is discussed. Oncolytic adenoviral delivery offers the potential benefits of restricted and renewable siRNA expression within the tumor microenvironment, an additive antitumor outcome through viral oncolysis and siRNA-mediated oncogene silencing, and a proven clinical platform with respect to infectivity and safety.

Adenoviridae↗

PubMed2004

Antisense oligonucleotides as a powerful molecular strategy for gene therapy in cardiovascular diseases.

Antisense oligonucleotides (ODN) technology is one of the most promising therapeutic strategies to prevent the progress of diseases through inhibiting the specific gene expression. They are well established to serve as molecular tools for several biologic applications, from the study of single gene function up to complex target validations. From the theoretical simple action, sequence-specific inhibition of mRNA functions after complex formation and presumably enzymatic degradation of the target mRNA, they obviously carry a high therapeutic potential to treat human diseases. In addition to the potential for the treatment, antisense ODN may be applicable for investigations of the mechanism and stereochemistry of biochemical reactions, mapping of nucleic acid protein interactions, and diagnostic applications. However, the design of antisense ODN, is very difficult because many factors affecting their activity and stability must be considered. Especially, the modifications of ODN are very critical and many researchers are trying to establish ODN which have resistance to nucleolytic degradation, high affinity to complementary nucleic acid, high selectivity in binding with complementary nucleic acid, the ability to activate ribonuclease H that selectively degrades the RNA strand of ODN-RNA complex, cell permeability, and favorable pharmacokinetic and pharmacodynamic attributes. In this review we would like to introduce some modifications of ODN design and examples of our applications of antisense ODN in cardiovascular disease in animal models.

Animals↗

PubMed1995

The efficacy and safety of isepamicin and ceftazidime compared with amikacin and ceftazidime in acute lower respiratory tract infection.

Isepamicin is a new aminoglycoside antibiotic which has a superior stability to aminoglycoside-inactivating enzymes compared with other available aminoglycosides. In this multicentre, randomised, open study, the safety and efficacy of isepamicin plus ceftazidime was compared with that of amikacin plus ceftazidime in adults with acute lower respiratory tract infection. Patients with severe infections received intravenous administration of isepamicin 15 mg/kg once daily + ceftazidime 2g twice daily (n = 121) or amikacin 7.5 mg/kg twice daily + ceftazidime 2g twice daily (n = 61). Those with less severe infection received intramuscular or intravenous administration of isepamicin 8 mg/kg once daily + ceftazidime 1g twice daily (n = 56) or amikacin 7.5 mg/kg twice daily + ceftazidime 1g twice daily (n = 28). In the efficacy populations, the proportion of patients clinically cured in the isepamicin group (87/100; 87%) was similar to that in the amikacin group (36/47; 77%). Significantly more patients in the isepamicin group were cured or improved compared with the amikacin group (97% vs 89%; p = 0.042). The difference between treatment groups was also significant in patients with pneumonia (p = 0.05). The most commonly isolated target organisms were Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus and Klebsiella pneumoniae. The proportion of patients in the efficacy population whose pretreatment valid target organisms were eliminated was similar in each treatment group (90% isepamicin vs 89% amikacin). A retrospective analysis showed there were slightly fewer clinical successes and a higher death rate in patients with nosocomial rather than community acquired pneumonia. Both treatments were well tolerated . Fourteen per cent of isepamicin and 11% of amikacin patients experienced adverse events. The incidence of ototoxicity and nephrotoxicity was low.

Acute Disease↗

PubMedDate not supplied

[Basic principles of the antisense strategy].

The antisens strategy is based on specific inhibition of the mutant gene expression by oligodeoxynucleotides (OGN), capable of selectively hybridizing with target DNA or RNA. Molecular mechanisms of the antisense oligonucleotide comprise: inhibition of splicing, inhibition of 5'-capping and 3'-polyadenylation, activation of RN-ase H, small interfering RNA, ribozymes. The antisense strategy is applied to: rational design of potent, selective therapeutic agents, target validation and detection of pathologic gene expression in vivo. The main aim of the antisense oligonucleotide design is to improve the affinity for target RNA and the resistance to nucleolytic degradation.

Enzyme Activation↗

PubMed2006

Mechanosensitive channels: therapeutic targets in the myocardium?

Mechanosensitivity is a property common to many cell types. Because channels gated by mechanical stimuli (mechanosensitive channels, MSCs) are implicated in many normal and pathological cellular responses, they present a valid target for therapeutic agents. However the process of mechanotranduction, the structure, function and pharmacology of eukaryotic MSCs are not well understood and matching experimental and in vivo stimuli is difficult. With respect to the pharmacology of these channels, a further complication arises because agents that modulate the activity of MSCs may not even bind to the channel itself, but may cause their effects by changing the properties of the tension-sensing lipid bilayer and/or cytoskeleton. MSCs in the myocardium are discussed in the context of their probable role in the generation of stretch-activated arrhythmias. The actions of the three most prominent agents used to study MSCs in the heart, the lanthanide gadolinium, the aminoglycosidic antibiotic streptomycin, and a peptide toxin isolated from tarantula venom, GsMTx-4, are compared. While all three can prevent mechanically-induced cardiac arrhythmias in experimental situations, only GsMTx-4 seems to have the potential as a novel therapeutic agent for the targeting of arrhythmias provoked by MSCs.

Anti-Arrhythmia Agents↗

PubMed2002

Surrogate endpoints in cancer drug development.

Over the next three years a large number of novel, mechanistically targeted drugs will enter clinical trials for cancer. The remarkable progress in understanding the molecular biology of cancer has provided an enormous range of validated targets for drug discovery. Following lead optimisation and suitable pharmaceutical formulation these compounds have undergone rapid screening in preclinical models. Innovative methods of clinical development are now essential to ensure optimal dose determination and scheduling. The discovery of novel surrogates for efficacy is essential in this fast moving area and requires imaginative partnerships between academic groups and the pharmaceutical industry.

Antineoplastic Agents↗