Research

Drug Discovery

Jump to: Drug induced kidney injury | Drug-membrane interaction | Drug-drug interactions | Chemoinformatics

 

Drug induced kidney injury

Nephrotoxicity, or damage to the kidney, is a side effect of many marketed drugs, with 19-25% of acute renal failures caused, in part, by drug exposure [1]. Many of these drugs are antibiotics, and include a number of classes that are the focus of drug discovery projects within the group. In the search for improved versions of existing drugs, and for the development of novel therapies, it would be very helpful to be able to screen for potential nephrotoxicity. Unfortunately, the gold standard for preclinical compound testing is kidney histopathology from animal studies, a low throughput and expensive procedure that requires sacrifice of the animal. In vivo monitoring of serum creatinine (SCr) or blood urea nitrogen (BUN) levels provides an alternative readout to kidney biopsies, but sensitivity and correlation to injury is poor. There has been an intensive effort in recent years to identify in vivo biomarkers that can be used to selectively monitor kidney damage [2-8]. In particular, proteins such as NGAL (Neutrophil gelatinase-associated lipocalin) [9] and Kim-1 (Kidney injury molecule-1) [7, 10] have been highlighted as proteins with much more relevance to early detection of kidney injury than traditional serum creatinine levels.

For drug discovery screening, a cell-based assay is much more useful than an in vivo assay, as potential liabilities can be assessed at a much earlier timepoint, and structure-activity relationships can be explored at a reasonable cost. There have been numerous research reports on the use of cellular assays systems to detect nephrotoxicity. However, the scope of these studies has been restricted by either the types of cells employed, the toxicity readouts assessed, or the drugs applied to the cells. Furthermore, the possible in vitro utility of many of the potential new in vivo biomarkers requires investigation.

We are undertaking a comprehensive research program using a matrix of cell types, reference compounds, and readouts to identify in vitro cellular assays that can be used to predict nephrotoxicity. We will investigate multiple human kidney-related cell types and compare the results to those seen in non-renal cells, allowing for the differentiation of general cytotoxicity from nephrotoxicity. We will test a range of known nephrotoxic and cytotoxic reference compounds. The cellular effects will be monitored using general cytotoxicity assays, biomarker-based assays, high content screening using fluorescent labelled markers, and label-free assays using both optical and electrical impedence biosensors. The results will provide us with an ability to counterscreen the group’s antibiotic drug discovery efforts for nephrotoxic side effects. In the future we hope to expand this effort to all drugs as a tool for the scientific and pharmaceutical research communities.

Figure 1. (a) Biomarkers of kidney injury and (b) Drugs that elicit site-specific toxicity [1]

 

[1] Bonventre, J.V.; et al., Nat. Biotechnol. 2010, 28, 436.

[2] Ozer, J.S.; et al., Nat. Biotechnol. 2010, 28, 486.

[3] Mattes, W.B.; et al., Nat. Biotechnol. 2010, 28, 432.

[4] Sistare, F.D.; et al., Nat. Biotechnol. 2010, 28, 446.

[5] Dieterle, F.; et al., Nat. Biotechnol. 2010, 28, 455.

[6] Dieterle, F.; et al., Nat. Biotechnol. 2010, 28, 463.

[7] Hoffmann, D.; et al., Toxicol. Sci. 2010, 116, 8.

[8] Yu, Y.; et al., Nat. Biotechnol. 2010, 28, 470

[9] Paragas, N.; et al., Nat. Med. 2011, 17, 216.

[10] Vaidya, V.S.; et al., Nat. Biotechnol. 2010, 28, 478.

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Drug-membrane interaction

All living cells are surrounded by one or more membranes. These membranes, composed of lipids and proteins, play important roles in cell survival and function. Drug design generally focuses on the interactions between ligands and their receptor or enzyme targets, and largely ignores the role played by cell membranes, particularly for membrane-based protein targets. However, knowledge of drug-membrane interactions is essential for understanding a drug’s biodistribution, activity, selectivity and toxicity.

The development of analytical tools for the study of drug-membrane interactions of increasing interest to scientists. Methods such as high-performance liquid chromatography (HPLC), fluorescence techniques and NMR are commonly used. We are undertaking several projects using surface plasmon resonance (SPR), cell impedance and resonant waveguide photonics; all label-free techniques, to investigate the interactions between novel antibiotics and cell membranes [1-5]. These provide an ideal model of cell membrane that can be varied to determine the binding affinity and kinetics of drugs on different membrane types. The results not only provide valuable information for drug design and development, but also contribute to investigations into the mode of action of novel antibiotics and cancer therapeutics.

 

[1] Cooper, M. A.; Williams, D. H., Chem. Biol. 1999, 6, 891.

[2] Cooper, M.A., Label-free biosensors : techniques and applications. 2009 Cambridge University Press: Cambridge.

[3] Chia, C. S.; Gong, Y.; Bowie, J. H.; Zuegg, J.; Cooper, M. A., Biopolymers. 2010, doi: 10.1022/bip.21438.

[4] Nussio, M. R.; Sykes, M. J.; Miners, J. O.; Shapter, J. G., ChemMedChem. 2007, 2, 366.

[5] Cooper, M.A., J. Mol. Recognit. 2004, 17, 286.

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Drug-drug interactions

With the general population now often taking more than one drug at the same time, adverse effects of drug-drug interactions are becoming very prominent. Knowing if there are side effects and changes in pharmacokinetics of a drug as a result of taking two different drugs at one time, is critical for drug efficacy. Pharmocokinetic interaction between drugs arise thereby if one drug changes the absorption, distribution, metabolism, or excretion of another drug, changing the concentration of active drugs in the body, in some case above their maximal tolerable dose.

Several systems are involved in changing the pharmacokinetic properties of a drug, including Cytochrome P450 and residence time on serum albumin. Inhibition of the CYP450 of one drug can change the metabolism of a second drug, whereas competitive binding to albumin affects the concentration and half-life of drugs in the blood. This research project is focusing on the development of fast, high throughput screening methods to investigate drug-drug interactions.

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Chemoinformatics

Chemoinformatic methods, generally described as computer and informational techniques in the field of chemistry, are nowadays essential tools in the discovery and development of new active compounds. In combination with databases such as chEMBL or PubChem, they provide essential information about existing compounds and compounds classes. But more importantly, using various statistical and predictive modeling tools Chemoinformatic methods are able to provide prediction on on- and off-target activity/selectivity and biochemical and pharmacokinetic properties (ADME-Tox)

The research project aims to develop and implement a comprehensive toolset and database for chemoinformatic. The main focus of the project will be the integration of molecular modelling (structural biology) and bioinformatic (molecular biology) methods with the chemoinformatic (chemistry) toolset.

For example, drug-target networks combine the sequence similarity between targets with the chemical similarity of their targets, to establish a wider relationship between structures and targets than would have been possible using only a single similarity relationship. Similarly, integrating structure docking and target homology procedures into the chemoinformatic toolsets will enhance its functionality.

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