SS 2008lecture 10 Biological Sequence Analysis 1 V10 Pharmacogenomics of P-Glycoprotein Review of lecture V9.. Paper on Pharmagenomics of PGP

SS 2008lecture 10 Biological Sequence Analysis 2 Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) Drug resistance of cells There are three major mechanisms of drug resistance in cells: (1)decreased uptake of water-soluble drugs such as folate antagonists, nucleoside analogues and cisplatin, which require transporters to enter cells; (2) various changes in cells that affect the capacity of cytotoxic drugs to kill cells, including alterations in cell cycle, increased repair of DNA damage, reduced apoptosis and altered metabolism of drugs; and (3) increased energy-dependent efflux of hydrophobic drugs that can easily enter the cells by diffusion through the plasma membrane.

SS 2008lecture 10 Biological Sequence Analysis 3 Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) Drug resistance of cells Of these mechanisms, the one that is most commonly encountered in the laboratory is the increased efflux of a broad class of hydrophobic cytotoxic drugs that is mediated by one of a family of energy-dependent transporters, known as ATP-binding cassette (ABC) transporters.

SS 2008lecture 10 Biological Sequence Analysis 4 human ABC transporters Based on sequence homology 48 different ABC transporters grouped into seven subfamilies have been defined in the human genome. Their functions range from export of cholesterol (ABCA1) to regulation of chloride current (ABCC7-CFTR). They also play roles in the absorption, distribution, and excretion of pharmacological compounds. P-glycoprotein (ABCB1 or MDR1): transports neutral or positively charged hydrophobic compounds. ABCC subfamily: also transports organic anions. Szakács et al. Cancer Cell 6, 129 (2004)

SS 2008lecture 10 Biological Sequence Analysis 5 Pharmacological roles of ABC transporters ATP-binding cassette (ABC) transporters act to prevent the absorption of orally ingested or airborne toxins, xenobiotics or drugs. Highly sensitive compartments, such as the brain, foetus or testes are protected by additional barriers. Enterohepatic circulation, as well as the excretion of compounds, is regulated by ABC transporters in the liver, gastrointestinal (GI) tract and the kidney. Although the systemic localization of ABC transporters at absorptive barriers provides an effective means to protect against dietary toxins, it also decreases the bioavailability of orally administered drugs and reduces drug disposition to physiological sanctuaries. BBB, blood–brain barrier; BCSFB, blood–cerebrospinal fluid barrier; CSF, cerebrospinal fluid. Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006)

SS 2008lecture 10 Biological Sequence Analysis 6 ABC transporters as drug exporters Given the high degree of similarity of ABCs equences, however, it seems plausible that additional members may also be drug exporters and thus be associated with decreased sensitivity of cancer anticancer drugs. To explore that proposition, Szakács et al. wanted to characterize ABC gene expression in a set of cancer cells whose responses to a large number of compounds are known and whose molecular characteristics have been cataloged. Szakács et al. Cancer Cell 6, 129 (2004)

SS 2008lecture 10 Biological Sequence Analysis 7 NCI-60  data set for a panel of 60 human cancer cell lines (the NCI-60) used by the Developmental Therapeutics Program (DTP) of the National Cancer Institute (NCI) to screen >100,000 chemical compounds since Included among the 60 cell lines are leukemias, melanomas, and cancers of ovarian, breast, prostate, lung, renal, colon, and central nervous system origin. Patterns of drug activity across the cell lines and patterns of cell sensitivity across the set of tested drugs have been shown to contain detailed information on mechanisms of action and resistance. In addition to this pharmacological characterization, the NCI-60 cells have been more extensively profiled at the DNA, mRNA, protein, and functional levels than any other set of cells in existence. Szakács et al. Cancer Cell 6, 129 (2004)

SS 2008lecture 10 Biological Sequence Analysis 8 Sanger Institute The Sanger institute is sequencing the NCI-60 for mutations in known human cancer genes. The cell lines were supplied by the NCI/NIH Developmental Therpeutics Program. The coding exons and immediate flanking intron sequences of selected genes from the Cancer Gene Census have been PCR amplified and sequenced.Census The results of this work have been entered in the COSMIC database and web site.COSMIC „All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred.“

SS 2008lecture 10 Biological Sequence Analysis 9 ABC transporter expression ABC transporter gene expression in the NCI-60 human cancer cell panel. The clustered image map shows patterns of gene expression assessed by real-time RT-PCR. Red and blue indicate high and low expression, respectively. The hierarchical clustering on each axis was done using the average-linkage algorithm with 1/r as the distance metric, where r is the Pearson’s correlation coefficient, after subtracting row and column means. Inset: highlights ABC transporters characteristically expressed in melanoma cells. Szakács et al. Cancer Cell 6, 129 (2004)

SS 2008lecture 10 Biological Sequence Analysis 10 Substrates and inhibitors of ABC transporters Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) Green: drug-gene pairs in which this ABC transporter was found to be overexpressed in these cell lines selected for resistance to the respective drug Red: resistant cells overexpressing a single ABC transporter often show characteristic cross-resistance to other, structurally unrelated drugs.

SS 2008lecture 10 Biological Sequence Analysis 11 Figure legend Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) Overlapping substrate specificities of the human ATP-binding cassette (ABC) transporters confering drug resistance to cancer cells. A single drug can be exported by several ABC transporters (rows), and each ABC transporter can confer characteristic resistance patterns to cells (columns). To determine which ABC transporters are involved in multidrug resistance (MDR), two different experimental procedures are common. Cells could be selected in increasing concentrations of a cytotoxic drug, which could result in the increased expression of a specific ABC transporter (see green boxes representing drug–gene pairs in which an ABC transporter was found to be overexpressed in cell lines selected for resistance to the respective drug). Resistant cells overexpressing a single ABC transporter often show characteristic cross- resistance to other, structurally unrelated, drugs (red boxes). Some ABC transporters were found to confer drug resistance only in transfection studies, in which cells are engineered to overexpress a given transporter. On transfection, cells become resistant to compounds that are substrates for transport (red boxes). White boxes denote unexplored or absent drug–gene relationships.

SS 2008lecture 10 Biological Sequence Analysis 12 Relationship between drug sensitivity and ABCB1 expression in the NCI-60 for a set of 118 drugs of putatively known mechanism of action. Blue : known ABCB1 substrates; red : compounds shown in previous studies not to be substrates of ABCB1; black bars : compounds for which data were not available from the literature. The drug names listed at the top and bottom are commonly used, representative agents from the classes shown by red and blue bars. Szakács et al. Cancer Cell 6, 129 (2004) Prediction for 118 drugs with known action The activity pattern of known substrates of ABCB1 is negatively correlated with the level of B1 expression. Other substances that are not transported by MDR1 are noncorrelated or positively correlated.

SS 2008lecture 10 Biological Sequence Analysis 13 Verification of novel ABCB1 substrates by follow-up studies. A: Scatter plot showing the correlation (r) of ABCB1 expression with sensitivity of the 60 cells to NSC B: MTT assay dose-response curves for treatment of KB-3-1 parental cancer cells and the selected resistant variant KBV1 with increasing concentrations of NSC KB-3-1: a human carcinoma cell line KB-V1: a multidrug resistant derivative of KB-3-1 that overexpresses MDR1-PGp PSC is an MDR1 antagonist. Szakács et al. Cancer Cell 6, 129 (2004) Predictions for 1400 further compounds Relevant for test!

SS 2008lecture 10 Biological Sequence Analysis 14 Prediction from the NCI-60 data of new substrates for ABCC2-MRP2 and ABCC11-MRP8, then validation of the predictions by MTT assay Szakács et al. Cancer Cell 6, 129 (2004) Further predictions of PGP substrates

SS 2008lecture 10 Biological Sequence Analysis 15 Prediction of 1 positively correlated compound! Prediction from the NCI-60 data, followed by independent verification, that the toxicity of NSC is potentiated, rather than inhibited, by expression of ABCB1 Szakács et al. Cancer Cell 6, 129 (2004)

SS 2008lecture 10 Biological Sequence Analysis 16 Conclusions Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) An ultimate goal in cancer therapy is to devise individually tailored treatment that targets growth-promoting pathways and circumvents drug resistance. In considering how to go about cataloguing important mechanisms of drug resistance in cancer, it makes sense to begin by focusing on the family of ABC transporters, as they are widely expressed in cancer cells and their capacity to confer drug resistance has been established, at least in vitro. Pgp represents one of the best-studied mechanisms of resistance to hydrophobic anticancer drugs. It remains to be seen whether other ABC transporters will emerge as culprits for treatment failure.

SS 2008lecture 10 Biological Sequence Analysis 17 Drug design to block ABC transporters Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) „Despite the clear rationale for the use of inhibitors of ABC transporters, especially of Pgp, the development of these products and demonstration of their efficacy has been slow. With a lack of marketable products, pharmaceutical companies have begun to lose interest. Only a few compounds are currently in clinical trials, as the development of most of the inhibitors (including valspodar (PSC-833), dexniguldipine, dextroverapamil and biricodar (VX-710)) has been discontinued.

SS 2008lecture 10 Biological Sequence Analysis 18 Drug design to block ABC transporters Szakács et al. Nat. Rev. Drug Disc. 5, 219 (2006) The bottleneck seems to be the unwelcome inhibition of ABC transporters at pharmacologically important locations. However, as more and more information about pharmacokinetic effects accumulate, new-generation inhibitors become more specific and potent (as shown through careful Pgp measurements and surrogate biological markers of Pgp inhibition). Ultimately, we anticipate that the efficacy of ABC transporter modulation will be established in a subset of human cancers. A clear-cut demonstration of the effectiveness of targeting Pgp will result in renewed interest and the development of further ABC transporter inhibitors will follow suit.“