Proteomic informatics: in silico methods lead to data management challenges

Proteomics, which identifies proteins and analyzes their function in cells, is foreseen as the next challenge in biomedicine as diseases in the body are most easily recognized through the function of their proteins. Achieving this recognition is more difficult than pure gene analysis: it is estimated that 35,000 genes are present in human DNA, encoding more than 1 million proteins. A myriad of in vitro and in silico technologies now exist for studying proteins and their biological function. This review focuses on the vast array of in silico proteomic analysis methods, highlights public and commercial repositories for this data, and discusses the challenges associated with resolving and integrating the knowledge originating from this data.     

The challenge of predicting drug toxicity in silico

Poor pharmacokinetics, side effects and compound toxicity are frequent causes of late-stage failures in drug development. A safe in silico identification of adverse effects triggered by drugs and chemicals would be highly desirable as it not only bears economical potential but also spawns a variety of ecological benefits: sustainable resource management, reduction of animal models and possibly less risky clinical trials. In computer-aided drug discovery, both existing and hypothetical compounds may be studied; the methods are fast, reproducible, and typically based on human bioregulators, making the question of transferability obsolete. In the recent past, our laboratory contributed towards the development of in silico concepts (--> multi-dimensional QSAR) and validated a series of "virtual test kits" based on the oestrogen, androgen, thyroid, and aryl hydrocarbon receptor (endocrine disruption, receptor-mediated toxicity) as well as on the enzyme cytochrome P450 3A4 (metabolic transformations, drug-drug interactions). The test kits are based on the three-dimensional structure of their target protein (i.e. ER(alphabeta), AR, TR(alphabeta), CYP450) or a surrogate thereof (AhR) and were trained using a representative selection of 362 substances. Subsequent evaluation of 107 compounds different therefrom showed that binding affinities are predicted close to experimental uncertainty. These results suggest that our approach is suited for the in silico identification of adverse effects triggered by drugs and chemicals and encouraged us to compile an Internet Database for the virtual screening of drugs and chemicals for toxic effects.     

The biochemistry and toxicity of atractyloside: a review

Atractyloside poisoning is an infrequent but often fatal form of herbal poisoning, which occurs worldwide but especially in Africa and the Mediterranean regions. The primary mechanism of atractyloside poisoning is known to be inhibition of the mitochondrial ADP transporter. Poisoning in humans may present with either acute hepatic or renal pathology and it is possible that there is a second, different mechanism of toxicity to the hepatocyte. Atractyloside in large amounts gives rise to massive necrosis, but in vitro studies have shown that at lower doses cells progress to apoptosis. Simple methods for the detection of atractyloside poisoning are at present restricted to thin-layer chromatography in urine and are useful only in the case of severe poisoning. Immunoassays, high-performance liquid chromatography, nuclear magnetic resonance, and a recently developed high-performance liquid chromatography/mass spectrometry method have yet to be applied to clinical diagnoses. There is at present no treatment, but a fuller understanding of the mechanisms of toxicity may lead to the application of a number of compounds that are effective in vitro.     

In silico ADME-Tox modeling: progress and prospects

Introduction: Although significant progress has been made in high-throughput screening of absorption, distribution, metabolism and excretion, and toxicity (ADME-Tox) properties in drug discovery and development, in silico ADME-Tox prediction continues to play an important role in facilitating the appropriate selection of candidate drugs by pharmaceutical companies prior to expensive clinical trials.

Areas covered: This review provides an overview of the available in silico models that have been used to predict the ADME-Tox properties of compounds. It also provides a comprehensive overview and summarization of the latest modeling methods and algorithms available for the prediction of physicochemical characteristics, ADME properties, and drug toxicity issues.

Expert opinion: The in silico models currently available have greatly contributed to the knowledge of screening approaches in the early stages of drug discovery and the development process. As the definitive goal of in silico molding is to predict the pharmacokinetics and disposition of compounds in vivo by assembling all kinetic processes within one global model, PBPK models can serve this purpose. However, much work remains to be done in this area to generate more data and input parameters to build more reliable and accurate prediction models.     

The modeling of alcohol consumption: a meta-analytic review

OBJECTIVE: Modeling, or the imitation of another's behavior, has been proposed to influence alcohol consumption. The literature dealing with effects of modeling on alcohol consumption was reviewed using meta-analytic procedures in order to determine the strength of the modeling effect and the variables that moderate the effect. METHOD: Thirteen studies were examined in which participant's alcohol consumption in the presence of a high consumption model was compared to a low consumption model condition or a no-model condition. Analyses were conducted for the four dependent measures utilized in the literature: amount consumed, blood alcohol concentration, number of sips taken and volume per sip. Mean effect sizes (d) were calculated for each dependent measure and moderator variables were examined. RESULTS: Modeling had a significant effect on all four dependent measures, with the strongest effects being on amount consumed and blood alcohol concentration. In addition, analyses identified numerous variables that moderate the effect of modeling on alcohol consumption, including the drinking history of the participant, the drinking task used and the nature of the interaction between model and participant. CONCLUSIONS: Results indicated that modeling has a strong effect on alcohol consumption; however, several variables do mediate this effect.     

Biosystems modelling for in silico target validation: challenges to implementation

Computer simulation of biological systems for in silico target validation has the potential for increasing the efficiency of pharmaceutical R&D by expanding the number of parameters tested ‘virtually’. Only the most interesting subset of these has to then be probed in vivo. By avoiding less informative experiments and focusing on variables with the greatest influence on clinical end points, valuable drug targets can be advanced more quickly and those with little or no leverage bypassed. With many compounds failing today due to insufficient efficacy, use of in silico methods should lead to a greater percentage of compounds making the transition to clinical drug. Though biosystems modelling has great advantages, the actual adoption and implementation within each organisation will be a variable process because it has a disruptive approach to current pharma R&D practices. Some companies may have scientific personnel, technical infrastructure and a management culture that provide fertile ground for such a change; other companies will likely struggle more than once to adopt such methods. Innovators need to understand the challenges to implementation they will face and what actions are likely to improve their chances of success. Organisations which successfully implement biosystems modelling for in silico target validation should be able to design experiments and trials more tailored to each drug target and thus achieve higher yields of approved drugs from compounds tested.     

Developmental toxicity of polychlorinated biphenyls (PCBs): a systematic review of experimental data

Experimental reproductive and developmental toxicity studies with polychlorinated biphenyls (PCBs) are reviewed in brief to determine their relevance for current environmental exposure of humans during the prenatal and postnatal developmental periods. Additional material is published in electronic form only, which contains graphic overviews on individual PCBs and various mixtures that are linked with the relevant citations. In this comprehensive article we focus on interactions of PCBs with biological substrates that could mediate adverse effects observed in experimental animals and in children, and the shortcomings of many of the animal studies available. A main point of criticism involves the relative lack of animal data on several of those persistent congeners, either as individual compounds or as environmentally relevant mixtures, which are currently used as a measure of human exposure. Experimental studies in animals are frequently conducted with commercial PCB mixtures, a test design that does not reflect the exposure situation in humans. Important improvements of animal experiments could be achieved by more complete reporting of litter data (pre- and post-natal losses, toxic signs in the dam and the offspring, birth weights and postnatal growth data), the inclusion of endpoints that have been found previously to be affected by PCBs, and measurements of internal exposure data.An erratum to this article can be found at     

Antimalarial drug toxicity: a review.

Malaria, caused mostly by Plasmodium falciparum and P. vivax, remains one of the most important infectious diseases in the world. Antimalarial drug toxicity is one side of the risk-benefit equation and is viewed differently depending upon whether the clinical indication for drug administration is malaria treatment or prophylaxis. Drug toxicity must be acceptable to patients and cause less harm than the disease itself. Research that leads to drug registration tends to omit two important groups who are particularly vulnerable to malaria--very young children and pregnant women. Prescribing in pregnancy is a particular problem for clinicians because the risk-benefit ratio is often very unclear. The number of antimalarial drugs in use is very small. Despite its decreasing efficacy against P. falciparum, chloroquine continues to be used widely because of its low cost and good tolerability. It remains the drug of first choice for treating P. vivax malaria. Pruritus is a common adverse effect in African patients. As prophylaxis, chloroquine is usually combined with proguanil. This combination has good overall tolerability but mouth ulcers and gastrointestinal upset are more common than with other prophylactic regimens. Sulfadoxine/pyrimethamine is well tolerated as treatment and when used as intermittent preventive treatment in pregnant African women. Sulfadoxine/pyrimethamine is no longer used as prophylaxis because it may cause toxic epidermal necrolysis and Stevens Johnson syndrome. Mefloquine remains a valuable drug for prophylaxis and treatment. Tolerability is acceptable to most patients and travellers despite the impression given by the lay press. Dose-related serious neuropsychiatric toxicity can occur; mefloquine is contraindicated in individuals with a history of epilepsy or psychiatric disease. Quinine is the mainstay for treating severe malaria in many countries. Cardiovascular or CNS toxicity is rare, but hypoglycaemia may be problematic and blood glucose levels should be monitored. Halofantrine is unsuitable for widespread use because of its potential for cardiotoxicity. There is renewed interest in two old drugs, primaquine and amodiaquine. Primaquine is being developed as prophylaxis, and amodiaquine, which was withdrawn from prophylactic use because of neutropenia and hepatitis, is a potentially good partner drug for artesunate against falciparum malaria. Atovaquone/proguanil is a new antimalarial combination with good efficacy and tolerability as prophylaxis and treatment. The most important class of drugs that could have a major impact on malaria control is the artemisinin derivatives. They have remarkable efficacy and an excellent safety record. They have no identifiable dose-related adverse effects in humans and only very rarely produce allergic reactions. Combining an artemisinin derivative with another efficacious antimalarial drug is increasingly being viewed as the optimal therapeutic strategy for malaria.     

Genetic toxicity of naphthalene: a review

Results of five previously unpublished studies of the genotoxicity of naphthalene are presented and extensively discussed in relation to the large database that exists in the published literature. According to the published literature, naphthalene has not induced gene mutations in bacterial assays or in a metabolically competent human cell line. However, naphthalene has caused cytotoxicity in some cell lines, and induced clastogenicity in Chinese hamster ovary (CHO) cells, in a human lymphoblastoid cell line, and in preimplantation mouse embryos. Some naphthalene metabolites were cytotoxic, but only naphthoquinones produced chromosomal damage in vitro. No chromosomal damage was observed in vivo in bone marrow erythrocytes from treated mice; however, a positive response was reported in a Drosophila assay for wing somatic mutation and recombination. The five unpublished studies of naphthalene genotoxicity include three studies in vitro (two Ames bacterial assays and an in vitro unscheduled DNA synthesis assay) and two in vivo (mouse micronucleus and in vivo unscheduled DNA synthesis). Naphthalene was inactive in all five studies, in agreement with reports in the published literature. Chronic inhalation of naphthalene over 2 yr induced an increased incidence of benign alveolar/bronchial adenomas in female mice, and nasal epithelial tumors in both sexes of rats. Inflammation, tissue damage, and subsequent regenerative hyperplasia at target organ sites occurred in both species. Results of standard genetic toxicity assays suggest that naphthalene is not likely to be genotoxic in vivo. Since the in vitro results come primarily from assays utilizing liver-mediated activation systems, and the in vivo results come from rodent organs that are not targets for tumors, tests using naphthalene-sensitive rodent tissues would determine the applicability of current data in addressing the mechanisms of these species and site-specific cancers. The standard assays reported here may be useful in predicting potential health hazard in other species, or in humans, in whom there are few reported instances of naphthalene-induced cancer, especially as more data on species-specific differences in naphthalene metabolism become available. Despite present data limitations, a threshold mechanism for tumorigenesis can be proposed. The absence of naphthalene-induced gene mutation and the presence of cytotoxicity and some chromosomal events in vitro are consistent with a threshold-related mechanism of tumor induction, driven by cytotoxicity and cell regeneration, followed by genetic events, or by accumulation of naphthalene at specific target sites to allow in situ formation of a genotoxic metabolite to trigger or enhance spontaneous tumor development.     

Predictive in silico modeling for hERG channel blockers

hERG-mediated sudden death as a side effect of non-antiarrhythmic drugs has been receiving increased regulatory attention. Perhaps owing to the unique shape of the ligand-binding site and its hydrophobic character, the hERG channel has been shown to interact with pharmaceuticals of widely varying structure. Several in silico approaches have attempted to predict hERG channel blockade. Some of these approaches are aimed primarily at filtering out potential hERG blockers in the context of virtual libraries, others involve understanding structure-activity relationships governing hERG-drug interactions. This review summarizes the most recent efforts in this emerging field.     

Insight into potential toxicity mechanisms of melamine: an in silico study

The toxicity of melamine has attracted much attention since the outbreak of nephrolithiasis among children ingesting melamine-contaminated infant formula in China. However, there is little knowledge about the molecular mechanisms underlying the melamine-induced toxicity. In this paper, a ligand-protein docking method (INVDOCK) was applied to predict the toxicity-related target proteins for melamine and its metabolite, cyanuric acid. As a result, 23 and 35 proteins were finally identified as the potential target proteins for melamine and cyanuric acid, respectively. Through an enrichment analysis, it was found that nephrotoxicity and lung toxicity might be the most significant toxicities induced by melamine and cyanuric acid. Four target proteins (glutathione peroxidase 1, beta-hexosaminidase subunit beta, L-lactate dehydrogenase and lysozyme C) may be related to the molecular basis of the nephrotoxicity induced by melamine except for known kidney crystals formation. After mapping all these toxicity-related target proteins onto cellular pathways, it was indicated that the toxicities of melamine and cyanuric acid might also be caused by breaking down redox balance, perturbing the arginine and proline metabolism and damaging the homeostasis of energy production system. To further explore the mechanisms underlying the toxicities of melamine and cyanuric acid, a biological signal cascades network constructed by some of the toxicity-related target proteins was discussed.     

From in vivo to in vitro/in silico ADME: progress and challenges

High-throughput screening technologies in biological sciences of large libraries of compounds obtained via combinatorial or parallel chemistry approaches, as well as the application of design rules for drug-likeness, have resulted in more hits to be evaluated with respect to their ADME or drug metabolism and pharmacokinetic properties. The traditional in vivo methods using preclinical species, such as rat, dog or monkey, are no longer sufficient to cope with this demand. This editorial discusses the changes towards medium- to high-throughput in vitro and in silico ADME screening. In addition, much more attention is now put on early safety and risk assessment of promising lead series and potential clinical candidates.