CDA: Combinatorial Drug Discovery Using Transcriptional Response Modules

<div><h3>Background</h3><p>Anticancer therapies that target single signal transduction pathways often fail to prevent proliferation of cancer cells because of overlapping functions and cross-talk between different signaling pathways. Recent research has identified that balanced multi-component therapies might be more efficacious than highly specific single component therapies in certain cases. Ideally, synergistic combinations can provide 1) increased efficacy of the therapeutic effect 2) reduced toxicity as a result of decreased dosage providing equivalent or increased efficacy 3) the avoidance or delayed onset of drug resistance. Therefore, the interest in combinatorial drug discovery based on systems-oriented approaches has been increasing steadily in recent years.</p> <h3>Methodology</h3><p>Here we describe the development of Combinatorial Drug Assembler (CDA), a genomics and bioinformatics system, whereby using gene expression profiling, multiple signaling pathways are targeted for combinatorial drug discovery. CDA performs expression pattern matching of signaling pathway components to compare genes expressed in an input cell line (or patient sample data), with expression patterns in cell lines treated with different small molecules. Then it detects best pattern matching combinatorial drug pairs across the input gene set-related signaling pathways to detect where gene expression patterns overlap and those predicted drug pairs could likely be applied as combination therapy. We carried out <em>in vitro</em> validations on non-small cell lung cancer cells and triple-negative breast cancer (TNBC) cells. We found two combinatorial drug pairs that showed synergistic effect on lung cancer cells. Furthermore, we also observed that halofantrine and vinblastine were synergistic on TNBC cells.</p> <h3>Conclusions</h3><p>CDA provides a new way for rational drug combination. Together with phExplorer, CDA also provides functional insights into combinatorial drugs. CDA is freely available at <a href="http://cda.i-pharm.org">http://cda.i-pharm.org</a>.</p> </div

Analysis pipeline of CDA.

<p>Combinatorial drug analysis process. In drug set pattern analysis step (the bottom right box), combinatorial drug analysis process treats profiles of two different molecules as a group to measure the synergistic effects of them.</p

Top 10 molecules showing similar expression patterns of transcriptional response modules to letrozole.

<p>Top 10 molecules showing similar expression patterns of transcriptional response modules to letrozole.</p

DRI values for the drug combinations at 25%, 50%, 75% levels of inhibition of A549 cell proliferation.

<p>DRI values for the drug combinations at 25%, 50%, 75% levels of inhibition of A549 cell proliferation.</p

Enriched pathway in lung adenocarcinoma.

<p>Enriched pathway in lung adenocarcinoma.</p

In vitro validation of halofantrine and vinblastine alone and in combination in a triple-negative breast cancer cell line.

<p>(A) Effects of halofantrine and vinblastine on MDA-MB-231 TNBC cell proliferation. IC₅₀ indicates the concentration of drug that induce 50% of inhibition of cell proliferation. (B) Halofantrine and vinblastine combination was treated in 2∶1 molar ratio. Halofantrine and vinblastine combination shows a strong synergistic effect. The IC₅₀ values of each drug in halofantrine-vinblastine combinations are 0.55 µM and 0.27 µM, respectively. The combination shows a strong synergistic effect (CI value is 0.12, and DRI values for halofantrine and vinblastine are 14.17 and 22.09, respectively).</p

Network map of halofantrine and vinblastine on triple-negative breast cancer using phExplorer.

<p>(A) It seems that halofantrine and vinblastine could affect on five different signaling pathways in TNBC. Group 5: Halofantrine- or vinblatine-related proteins which are also related with proteins of A6B1 and A6B4 Integrin signaling pathway. Group 6: Proteins which are related with vinblasitne as well as proteins of EGFR family signaling pathways (such as ERBB1 signaling pathway, ERBB2/ERBB3 signaling events, ERBB4 signaling events, ERBB receptor signaling network). (B) We hypnotized that halofantrine and vinblastine are synergistic because they complementary regulate integrin and EGFR signaling pathways. Group 0: A part of EGFR family signaling pathways. Group 1: A part of A6B1 and A6B4 Integrin signaling pathway.</p

Synergistic combinatorial drug pairs on lung cancer cells.

<p>(A, B) Effects of alsterpaullone, scriptaid, irinotecan, and semustine on A549 cancer cell proliferation. IC₅₀ indicates the concentration of drug that induce 50% of inhibition of cell proliferation. Error bars represent the standard deviation of six experiments. (C, D) Drug pairs were treated in 1∶1 molar ratio. The IC₅₀ values of each drug are plotted on the axes, and the dashed line represents addictive effect. Triangle point represents the concentrations of the combinations resulting in 50% of proliferation inhibition. As the triangle points are positioned on the left of the dashed line, these combinatorial drug pairs are synergistic. The IC₅₀ values of each drug in alsterpaullone-scriptaid and irinotecan-semustine combinations are 0.65 µM and 26.05 µM, respectively.</p

Azobenzene Molecular Machine: Light-Induced Wringing Gel Fabricated from Asymmetric Macrogelator

To develop light-triggered wringing gels, an asymmetric macrogelator (1AZ3BP) was newly synthesized by the chemically bridging a photoisomerizable azobenzene (1AZ) molecular machine and a biphenyl-based (3BP) dendron with a 1,4-phenylenediformamide connector. 1AZ3BP was self-assembled into a layered superstructure in the bulk state, but 1AZ3BP formed a three-dimensional (3D) network organogel in solution. Upon irradiating UV light onto the 3D network organogel, the solvent of the organogel was squeezed and the 3D network was converted to the layered morphology. It was realized that the metastable 3D network organogels were fabricated mainly due to the nanophase separation in solution. UV isomerization of 1AZ3BP provided sufficient molecular mobility to form strong hydrogen bonds for the construction of the stable layered superstructure. The light-triggered wringing gels can be smartly applied in remote-controlled generators, liquid storages, and sensors