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<script type="text/javascript" src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.boots.min.js"> </script><title>Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1 - Probe Reports from the NIH Molecular Libraries Program - NCBI Bookshelf</title>
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<meta name="citation_inbook_title" content="Probe Reports from the NIH Molecular Libraries Program [Internet]">
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<meta name="citation_title" content="Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1">
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<meta name="citation_publisher" content="National Center for Biotechnology Information (US)">
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<meta name="citation_date" content="2013/02/28">
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<meta name="citation_author" content="Leigh Carmody">
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<meta name="citation_author" content="Andrew Germain">
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<meta name="citation_author" content="Barbara Morgan">
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<meta name="citation_author" content="Lynn VerPlank">
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<meta name="citation_author" content="Cristina Fernandez">
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<meta name="citation_author" content="Erin Forbeck">
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<meta name="citation_author" content="Amal Ting">
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<meta name="citation_author" content="Yuxiong Feng">
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<meta name="citation_author" content="Jose Perez">
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<meta name="citation_author" content="Sivaraman Dandapani">
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<meta name="citation_author" content="Benito Munoz">
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<meta name="citation_author" content="Michelle Palmer">
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<meta name="citation_author" content="Eric Lander">
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<meta name="citation_author" content="Piyush B. Gupta">
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<meta name="citation_author" content="Stuart L. Schreiber">
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<meta name="citation_pmid" content="23658966">
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<meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK133423/">
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<link rel="schema.DC" href="http://purl.org/DC/elements/1.0/">
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<meta name="DC.Title" content="Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1">
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<meta name="DC.Type" content="Text">
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<meta name="DC.Publisher" content="National Center for Biotechnology Information (US)">
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<meta name="DC.Contributor" content="Leigh Carmody">
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<meta name="DC.Contributor" content="Andrew Germain">
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<meta name="DC.Contributor" content="Barbara Morgan">
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<meta name="DC.Contributor" content="Lynn VerPlank">
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<meta name="DC.Contributor" content="Cristina Fernandez">
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<meta name="DC.Contributor" content="Erin Forbeck">
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<meta name="DC.Contributor" content="Amal Ting">
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<meta name="DC.Contributor" content="Yuxiong Feng">
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<meta name="DC.Contributor" content="Jose Perez">
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<meta name="DC.Contributor" content="Sivaraman Dandapani">
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<meta name="DC.Contributor" content="Benito Munoz">
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<meta name="DC.Contributor" content="Michelle Palmer">
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<meta name="DC.Contributor" content="Eric Lander">
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<meta name="DC.Contributor" content="Piyush B. Gupta">
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<meta name="DC.Contributor" content="Stuart L. Schreiber">
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<meta name="DC.Date" content="2013/02/28">
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<meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK133423/">
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<meta name="description" content="Cancer stem cells (CSCs), which drive tumor growth, are known to be resistant to standard chemotherapy and radiation treatment. This raises a significant unmet need to find therapies that can target CSCs within tumors because these cells are responsible for recurrence, the primary cause of patient mortality. However, one of the challenges is that CSCs are not stable outside the tumor environment and are not easy to grow in culture media. Hence, stable sibling cell lines that were induced into epithelial-to-mesenchymal transdifferentiation (EMT) to stably propagate CSC-enriched populations were used to screen a library of 300,718 compounds from the Molecular Libraries Small Molecule Repository (MLSMR). Several classes of selective inhibitors of CSCs were identified. The use of isogenic control cell lines for the secondary validation assays minimized the probability of false hits advancing along the critical path to probe development. Of these, 19 compounds were chosen based on their selectivity, potency, and chemical tractability and were retested in the primary screen and secondary assays. Three scaffolds were prioritized to identify potential probes. One of these compounds (ML239) displayed greater than 23-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control cell line (HMLE_sh_GFP). This probe did not significantly inhibit tumorsphere formation in the breast cancer cell line SUM159, which is a mixture of CSCs and differentiated cells. However, analogs that inhibited both cell types (HMLE_sh_Ecad and HMLE_sh_GFP) could suppress tumorsphere formation, suggesting that suppression of both cell types may be needed to inhibit tumorsphere formation in the SUM159 cancer cell line. Gene expression experiments where HMLE_sh__Ecad cells were treated with the probe (ML239) identified protein processing genes in the endoplasmic reticulum (ER) (i.e., Sels, HSPAS, ATF4, GADD23, and HERPUD1), Ras-mitogen-activated protein kinase (MAPK) signaling (i.e., CREB2(ATF-4); GADD153), and inflammatory cytokine expression/signaling pathways (i.e., IL-6) as having altered expression after treatment with the probe. Only five genes had significantly altered gene expression changes after 24-hour treatment with the probe in the HMLE_sh_GFP cell line. This further supports the finding that we have identified a selective probe that targets breast CSC-like cells. This new probe should be useful in future, cell-based investigations and in vivo studies of breast cancer models as well as target identification studies.">
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<meta name="og:title" content="Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1">
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<meta name="og:type" content="book">
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<meta name="og:description" content="Cancer stem cells (CSCs), which drive tumor growth, are known to be resistant to standard chemotherapy and radiation treatment. This raises a significant unmet need to find therapies that can target CSCs within tumors because these cells are responsible for recurrence, the primary cause of patient mortality. However, one of the challenges is that CSCs are not stable outside the tumor environment and are not easy to grow in culture media. Hence, stable sibling cell lines that were induced into epithelial-to-mesenchymal transdifferentiation (EMT) to stably propagate CSC-enriched populations were used to screen a library of 300,718 compounds from the Molecular Libraries Small Molecule Repository (MLSMR). Several classes of selective inhibitors of CSCs were identified. The use of isogenic control cell lines for the secondary validation assays minimized the probability of false hits advancing along the critical path to probe development. Of these, 19 compounds were chosen based on their selectivity, potency, and chemical tractability and were retested in the primary screen and secondary assays. Three scaffolds were prioritized to identify potential probes. One of these compounds (ML239) displayed greater than 23-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control cell line (HMLE_sh_GFP). This probe did not significantly inhibit tumorsphere formation in the breast cancer cell line SUM159, which is a mixture of CSCs and differentiated cells. However, analogs that inhibited both cell types (HMLE_sh_Ecad and HMLE_sh_GFP) could suppress tumorsphere formation, suggesting that suppression of both cell types may be needed to inhibit tumorsphere formation in the SUM159 cancer cell line. Gene expression experiments where HMLE_sh__Ecad cells were treated with the probe (ML239) identified protein processing genes in the endoplasmic reticulum (ER) (i.e., Sels, HSPAS, ATF4, GADD23, and HERPUD1), Ras-mitogen-activated protein kinase (MAPK) signaling (i.e., CREB2(ATF-4); GADD153), and inflammatory cytokine expression/signaling pathways (i.e., IL-6) as having altered expression after treatment with the probe. Only five genes had significantly altered gene expression changes after 24-hour treatment with the probe in the HMLE_sh_GFP cell line. This further supports the finding that we have identified a selective probe that targets breast CSC-like cells. This new probe should be useful in future, cell-based investigations and in vivo studies of breast cancer models as well as target identification studies.">
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match">◀</a><button id="jr-fip-matches">no matches yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK133423_"><span class="title" itemprop="name">Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1</span></h1><p class="contribs">Carmody L, Germain A, Morgan B, et al.</p><p class="fm-aai"><a href="#_NBK133423_pubdet_">Publication Details</a></p></div></div><div class="jig-ncbiinpagenav body-content whole_rhythm" data-jigconfig="allHeadingLevels: ['h2'],smoothScroll: false" itemprop="text"><div id="_abs_rndgid_" itemprop="description"><p>Cancer stem cells (CSCs), which drive tumor growth, are known to be resistant to standard chemotherapy and radiation treatment. This raises a significant unmet need to find therapies that can target CSCs within tumors because these cells are responsible for recurrence, the primary cause of patient mortality. However, one of the challenges is that CSCs are not stable outside the tumor environment and are not easy to grow in culture media. Hence, stable sibling cell lines that were induced into epithelial-to-mesenchymal transdifferentiation (EMT) to stably propagate CSC-enriched populations were used to screen a library of 300,718 compounds from the Molecular Libraries Small Molecule Repository (MLSMR). Several classes of selective inhibitors of CSCs were identified. The use of isogenic control cell lines for the secondary validation assays minimized the probability of false hits advancing along the critical path to probe development. Of these, 19 compounds were chosen based on their selectivity, potency, and chemical tractability and were retested in the primary screen and secondary assays. Three scaffolds were prioritized to identify potential probes. One of these compounds (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=abstract&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) displayed greater than 23-fold selective inhibition of the breast CSC-like cell line (HMLE_sh_Ecad) over the isogenic control cell line (HMLE_sh_GFP). This probe did not significantly inhibit tumorsphere formation in the breast cancer cell line SUM159, which is a mixture of CSCs and differentiated cells. However, analogs that inhibited both cell types (HMLE_sh_Ecad and HMLE_sh_GFP) could suppress tumorsphere formation, suggesting that suppression of both cell types may be needed to inhibit tumorsphere formation in the SUM159 cancer cell line. Gene expression experiments where HMLE_sh__Ecad cells were treated with the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=abstract&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) identified protein processing genes in the endoplasmic reticulum (ER) (i.e., Sels, HSPAS, ATF4, GADD23, and HERPUD1), Ras-mitogen-activated protein kinase (MAPK) signaling (i.e., CREB2(ATF-4); GADD153), and inflammatory cytokine expression/signaling pathways (i.e., IL-6) as having altered expression after treatment with the probe. Only five genes had significantly altered gene expression changes after 24-hour treatment with the probe in the HMLE_sh_GFP cell line. This further supports the finding that we have identified a selective probe that targets breast CSC-like cells. This new probe should be useful in future, cell-based investigations and <i>in vivo</i> studies of breast cancer models as well as target identification studies.</p></div><div class="h2"></div><p><b>Assigned Assay Grant No.:</b> 1 R03 MH089663-01</p><p><b>Screening Center Name and PI:</b> Broad Institute Probe Development Center, Stuart Schreiber</p><p><b>Chemistry Center Name and PI:</b> Broad Institute Probe Development Center, Stuart Schreiber</p><p><b>Assay Submitter and Institution:</b> Eric Lander, Broad Institute and Piyush Gupta, Whitehead Institute</p><p><b>PubChem Summary Bioassay Identifier:</b>
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<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/2721" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 2721</a></p><div id="ml239.s1"><h2 id="_ml239_s1_">Probe Structure & Characteristics</h2><div id="ml239.fu1" class="figure bk_fig"><div class="graphic"><img src="/books/NBK133423/bin/ml239fu1.jpg" alt="ML239." /></div><h3><span class="title"><a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a></span></h3></div><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figml239tu1"><a href="/books/NBK133423/table/ml239.tu1/?report=objectonly" target="object" title="Table" class="img_link icnblk_img figpopup" rid-figpopup="figml239tu1" rid-ob="figobml239tu1"><img class="small-thumb" src="/books/NBK133423/table/ml239.tu1/?report=thumb" src-large="/books/NBK133423/table/ml239.tu1/?report=previmg" alt="Image " /></a><div class="icnblk_cntnt"><h4 id="ml239.tu1"><a href="/books/NBK133423/table/ml239.tu1/?report=objectonly" target="object" rid-ob="figobml239tu1">Table</a></h4></div></div></div><div id="ml239.s2"><h2 id="_ml239_s2_">1. Recommendations for Scientific Use of the Probe</h2><p>There is an obvious unmet need for developing breast cancer stem cell (CSC)-selective compounds. Breast CSCs are thought to be responsible for cancer recurrence and resistance to chemotherapeutic treatments. Developing probes against breast CSCs enables researchers to gain a better perspective and a pathway to targeting these cells in the clinic.</p><p>Nine small molecules have been identified to selectively inhibit breast CSCs. Only one molecule, salinomycin, has been identified to selectively inhibit this particular breast CSC-like cell line (HMLE_sh_Ecad). Although it has a potency of approximately 1 μM against this cell line, it should be noted that salinomycin also shows toxicity against the control cell line (HMLE_sh_GFP) at 10 μM (<a class="figpopup" href="/books/NBK133423/figure/ml239.f2/?report=objectonly" target="object" rid-figpopup="figml239f2" rid-ob="figobml239f2">Figure 2</a>). Therefore, the goal of this project is to find a potent probe with less toxicity liability to control cell lines.</p><p>In addition to the clinical value, these probes have the potential to be used for novel target identification. The current body of work identifies numerous genes whose expression is modified by treatment with the probe (CID 49843203/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>). Treatment of the HMLE_sh_Ecad cell line identified changes in several cellular processes, such as protein processing genes in the ER (i.e., Sels, HSPAS, ATF4, GADD23, and HERPUD1), MAPK signaling (i.e., CREB2(ATF-4); GADD153), and inflammatory cytokine expression/signaling pathways (i.e., IL-6). Furthermore, this probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) is currently being optimized for use in binding studies with the intent of identifying direct molecular targets within the cell. The identification of a molecular target will allow for better probe development and open a new line of biological inquiry into the relevance of breast CSCs. Based on stability studies in PBS (<a href="#ml239.s12">Section 2.2</a>), the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) is suitable for assays dosing for three days or shorter.</p></div><div id="ml239.s3"><h2 id="_ml239_s3_">2. Materials and Methods</h2><div id="ml239.s4"><h3>2.1. Assays</h3><div id="ml239.s5"><h4>Primary HTS Using CellTiter-Glo (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/2717" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 2717</a>)</h4><p>HMLE_sh_Ecad cells were prepared as previously described (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>).</p><p><b>Procedures:</b> Briefly, HMLE cells expressing either shRNA targeting E-cadherin (HMLE_sh_Ecad) were propagated in 1:1 mixture of 10% fetal bovine serum (FBS; HyClone), 1% Penicillin/Streptomycin (Pen/Strep; Cellgro), 1% Glutamax-1 (Invitrogen), 70 nM Hydrocortisone (Sigma), 12 μg/ml Insulin (Sigma), 50 μg/ml Gentamicin (Sigma), 12.5 μg/ml Plasmocin (InVivogen), 10 ng/ml EGF in DMEM (Cellgro) with Mammary Epithelial Cell Growth Medium (MEGM complete medium; Lonza, Basel, Switzerland) at 37 ºC, 5% CO<sub>2</sub>. For screening, the cells were counted and resuspended in complete media without serum. Next, 2,000 cells in 50 μl were plated per well in white, tissue culture-treated, 384-well plates (Corning). The cells were incubated at 37 ºC, 5% CO<sub>2</sub> for at least 4 hours and pinned with 100 nl of compounds. The cells were incubated approximately 72 hours, then 30 μl of CellTiter-Glo (Promega) diluted 1:3 with PBS was added to the well. The plates were read using the EnVision (PerkinElmer; Luminescence 0.1 sec/well) after 12 minutes.</p></div><div id="ml239.s6"><h4>Primary Retest (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/449748" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 449748</a>)</h4><p>Repeat of the primary screen at dose using CellTiter-Glo.</p></div><div id="ml239.s7"><h4>Primary Cell Viability Protocol with HMLE_sh_Ecad Cells Using CellTiter-Glo (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493226" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493226</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493176" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493176</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504449" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504449</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504535" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504535</a>)</h4><p><b>Procedures:</b> Briefly, HMLE cells expressing either shRNA targeting E-cadherin (HMLE_sh_Ecad), control shRNA targeting GFP (HMLE_sh_GFP), or shRNA targeting Twist (sh_Twist) were propagated in 1:1 mixture of 10% FBS (HyClone), 1% Penicillin/Streptomycin (Pen/Strep; Cellgro), 1% Glutamax-1 (Invitrogen), 70 nM Hydrocortisone (Sigma), 12 μg/ml Insulin (Sigma), 50 μg/ml Gentamicin (Sigma), 12.5 μg/ml Plasmocin (InVivogen), 10 ng/ml EGF in DMEM (Cellgro) with Mammary Epithelial Cell Growth Medium (MEGM complete medium; Lonza, Basel, Switzerland) at 37 ºC, 5% CO<sub>2</sub>. For screening, the cells were counted and resuspended in complete media without serum. Next, 2,000 cells in 50 μl were plated per well in white, tissue culture-treated, 384-well plates (Corning). The cells were incubated at 37 ºC, 5% CO<sub>2</sub> for at least 4 hours and pinned with 100 nl of compounds. The cells were incubated approximately 72 hours, then 30 μl of CellTiter-Glo (Promega) diluted 1:3 with PBS was added to the well. The plates were read using the EnVision (PerkinElmer; Luminescence 0.1 sec/well) after 12 minutes.</p></div><div id="ml239.s8"><h4>Secondary Cell Viability Protocol with HMLE_sh_GFP Cells Using CellTiter-Glo (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504325" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504325</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493196" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493196</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504450" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504450</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504533" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504533</a>)</h4><p>HMLE cells expressing control shRNA targeting GFP (HMLE_sh_GFP) were prepared as previously described (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>).</p></div><div id="ml239.s9"><h4>Assay Provider Cell Viability Protocol with CellTiter-Glo (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/588704" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 588704</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/588703" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 588703</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/588702" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 588702</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/588705" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 588705</a>)</h4><p>HMLE cells expressing shRNA targeting Twist (HMLE_sh_TWIST), HMLE_sh_Ecad, HMLE_sh_GFP, and MDA231 cells were derived and propagated as previously described (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>).</p></div><div id="ml239.s10"><h4>Secondary Orthogonal Assay for <i>In Vitro</i> Inhibition of Tumorspheres with Sum159 HMLER Cells (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504623" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504623</a>)</h4><p>Sum159 cells were provided by the Assay Provider as previously described (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>).</p><p><b>Procedures:</b> Tumorsphere assays were performed as previously described (<a class="bibr" href="#ml239.r8" rid="ml239.r8">8</a>) with minor changes. Sum159 cells were propagated in 5% FBS (HyClone), 1 % Pen/Strep, 1% Glutamax-1, 12 μg/ml Insulin, 50 μg/ml Gentamicin in F12/DMEM (Cellgro). Next, 96-well, ultra-low adhesion plates (Costar) were plated with 100 μl media respective to cell type. Then, 400 nl of compounds were pinned into the media. The cells were harvested, counted, and resuspended in their propagation media with 1% methylcellulose (ES-CultM3120, Stem Cell Technologies). Then, 100 μl of resuspended cells were added to the plates containing media with compound for a final count of 2000 cells/well in 200 μl with 0.5% methylcellulose. Tumorspheres were allowed to form for 9 days incubated at 37 °C, 5% CO<sub>2</sub>. Tumorspheres were imaged using a 2× objective on the ImageXpress Micro (Molecular Devices, Sunnyvale, CA). Cell clusters greater than 100 μM in diameter were identified using MetaXpress software (version 3.1; Molecular Devices).</p></div><div id="ml239.s11"><h4>Gene Expression Assays with HMLE_sh_Ecad and HMLE_sh_GFP Cells (<a href="http://www.ebi.ac.uk/arrayexpress/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">http://www.ebi.ac.uk/arrayexpress/</a> accession # E-MTAB-884)</h4><p>Duplicate samples of HMLE_sh_Ecad and HMLE_sh_GFP cells were treated with vehicle (DMSO) or compound at an IC<sub>80</sub> dose for 6 hours or 24 hours prior to isolation of RNA. Total RNA was isolated using the RNeasy Protect Mini Kit (Qiagen). Quality control (QC), processing of the RNA samples and the gene expression analysis were performed by the Genome Analysis Platform (GAP) at the Broad Institute.</p><p><b>Procedures:</b> Briefly, RNA samples were analyzed for quality using Aglient Bioanalyzer Chips. cRNA synthesis from the total RNA samples passing QC was prepared for analysis on a HumanHT-12 Expression BeadChip (Illumina, San Diego, CA) according to the manufacturer’s instructions. Normalization of the raw gene expression data, QC checks, and analyses were done with GenomeStudio (version 2010.3; Illumina, San Diego, CA). Replicate samples were normalized using cubic spline normalization, with the exception of HMLE_sh_Ecad 0 hrs (ECad0) of treatment. One sample of HMLE_sh_Ecad_0 hrs failed QC controls affecting the overall levels of total gene expression and significantly lower probe annealing samples. This sample was excluded from analysis, and the single remaining sample was used in comparison studies. After the samples were normalized, genes were selected as having greater than 2× change in expression levels.</p></div></div><div id="ml239.s12"><h3>2.2. Probe Chemical Characterization</h3><p>After preparation as described in <a href="#ml239.s13">Section 2.3</a>, the probe (CID 49835877/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>/<a href="https://pubchem.ncbi.nlm.nih.gov/substance/114279607" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">SID 114279607</a>) was analyzed by UPLC, <sup>1</sup>H and <sup>13</sup>C NMR spectroscopy, and high-resolution mass spectrometry. The data obtained from NMR and mass spectroscopy were consistent with the structure of the probe, and UPLC indicated an isolated purity of 93%.</p><p>The solubility of the probe (CID 49835877/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) was experimentally determined to be 6.3 μM in Phosphate buffered saline (PBS) solution. The probe is stable, with 76.7% remaining after a 48-hour incubation period. The data from the PBS stability assay is provided in <a class="figpopup" href="/books/NBK133423/figure/ml239.f1/?report=objectonly" target="object" rid-figpopup="figml239f1" rid-ob="figobml239f1">Figure 1</a>. Plasma protein binding (PPB) was determined to be 98.8% bound in human plasma. The probe is modestly stable to human plasma, with approximately 49.2% remaining after a 5-hour incubation period. The compound was found to be stable in glutathione (GSH) with 85.1% remaining after 48 hours.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figml239f1" co-legend-rid="figlgndml239f1"><a href="/books/NBK133423/figure/ml239.f1/?report=objectonly" target="object" title="Figure 1" class="img_link icnblk_img figpopup" rid-figpopup="figml239f1" rid-ob="figobml239f1"><img class="small-thumb" src="/books/NBK133423/bin/ml239f1.gif" src-large="/books/NBK133423/bin/ml239f1.jpg" alt="Figure 1. Stability Data for the Probe (CID 49835877/ML239) in PBS Plus Acetonitrile Over 48 Hours." /></a><div class="icnblk_cntnt" id="figlgndml239f1"><h4 id="ml239.f1"><a href="/books/NBK133423/figure/ml239.f1/?report=objectonly" target="object" rid-ob="figobml239f1">Figure 1</a></h4><p class="float-caption no_bottom_margin">Stability Data for the Probe (CID 49835877/ML239) in PBS Plus Acetonitrile Over 48 Hours. </p></div></div><p>The stability of the probe (CID 49835877/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) in PBS (0.1% DMSO) was measured over 48 hours. We noticed that the concentration of the probe steadily increased over 48 hours to about 3000% relative to the concentration at the start of the experiment (data not shown). Since the solubility of the probe in PBS is low, we believe that the gradual increase in concentration is the direct result of more of the compound dissolving in PBS over time. In other words, when we performed the PBS stability assay under the recommended conditions, we measured the kinetic solubility of the probe in PBS and not its stability. Thus, we decided to determine the total amount of the probe present in the well after the probe was treated with PBS alone for a given length of time. We added acetonitrile at various time points to wells containing the probe in PBS and measured the total amount of the probe. This result is shown in <a class="figpopup" href="/books/NBK133423/figure/ml239.f1/?report=objectonly" target="object" rid-figpopup="figml239f1" rid-ob="figobml239f1">Figure 1</a>. From these results, the probe seems to be stable in PBS since more than 76% is still present after 48 hours of incubation.</p></div><div id="ml239.s13"><h3>2.3. Probe Preparation</h3><p>The probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) was synthesized from 2-(2,4,6-trichlorophenoxy)acetohydrazide and 1<i>H</i>-pyrrole-2-carbaldehyde in one step (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f5/?report=objectonly" target="object" rid-figpopup="figml239f5" rid-ob="figobml239f5">Scheme 1</a>). Heating the two components in ethanol in the presence of magnesium sulfate at 40 °C for 8 hours provided the probe (<i>E</i>)-<i>N</i>′-((1<i>H</i>-pyrrol-2-yl)methylene)-2-(2,4,6-trichlorophenoxy)acetohydrazide in 65% yield.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figml239f5" co-legend-rid="figlgndml239f5"><a href="/books/NBK133423/figure/ml239.f5/?report=objectonly" target="object" title="Scheme 1" class="img_link icnblk_img figpopup" rid-figpopup="figml239f5" rid-ob="figobml239f5"><img class="small-thumb" src="/books/NBK133423/bin/ml239f5.gif" src-large="/books/NBK133423/bin/ml239f5.jpg" alt="Scheme 1. Synthesis of the Probe (CID49843203/ML239)." /></a><div class="icnblk_cntnt" id="figlgndml239f5"><h4 id="ml239.f5"><a href="/books/NBK133423/figure/ml239.f5/?report=objectonly" target="object" rid-ob="figobml239f5">Scheme 1</a></h4><p class="float-caption no_bottom_margin">Synthesis of the Probe (CID49843203/ML239). </p></div></div><div id="ml239.s14"><h4>Chemistry Experimental Methods</h4><p><b>General details.</b> All oxygen and/or moisture-sensitive reactions were carried out under N<sub>2</sub> atmosphere in glassware that had been flame-dried under vacuum (approximately 0.5 mm Hg) and purged with nitrogen (N<sub>2</sub>) prior to use. All reagents and solvents were purchased from commercial vendors and used as received, or synthesized according to methods already reported. NMR spectra were recorded on a Bruker 300 (300 MHz <sup>1</sup>H, 75 MHz <sup>13</sup>C) or Varian UNITY INOVA 500 (500 MHz <sup>1</sup>H, 125 MHz <sup>13</sup>C) spectrometer. Proton and carbon chemical shifts are reported in ppm (δ) referenced to the NMR solvent. Data are reported as follows: chemical shifts, multiplicity (br = broad, s = singlet, d = doublet, t = triplet, q = quartet, m = multiplet; coupling constant(s) in Hz).</p><p>Unless otherwise indicated, NMR data were collected at 25 °C. Flash chromatography was performed using 40–60 μm Silica Gel (60 Å mesh) on a Teledyne Isco Combiflash R<sub><i>f</i></sub>. Tandem Liquid Chromatography/Mass Spectrometry (LC/MS) was performed on a Waters 2795 separations module and 3100 mass detector. Analytical thin layer chromatography (TLC) was performed on EM Reagent 0.25 mm silica gel 60-F plates. Visualization was accomplished with ultraviolet (UV) light and aqueous potassium permanganate (KMnO<sub>4</sub>) stain followed by heating. High-resolution mass spectra were obtained at the MIT Mass Spectrometry Facility (Bruker Daltonics APEXIV 4.7 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer).</p><p>2-(2,4,6-Trichlorophenoxy)acetohydrazide (50 mg, 0.19 mmol), 1<i>H</i>-pyrrole-2-carbaldehyde (35 mg, 0.37 mmol) and magnesium sulfate (45 mg, 0.37 mmol) were dissolved in ethanol (1.5 mL). The reaction mixture was heated to 40 °C and stirred for 8 hours. The reaction was taken up in ethyl acetate (50 mL) and washed with water (2 × 25 mL) followed by brine (1 × 25 mL). The combined organic layers were dried over sodium sulfate (Na<sub>2</sub>SO<sub>4</sub>), filtered, and concentrated. Purification by column chromatography provided (<i>E</i>)-<i>N</i>′-((1<i>H</i>-pyrrol-2-yl)methylene)-2-(2,4,6-trichlorophenoxy)acetohydrazide as a light yellow solid (41 mg, 65% yield).</p><p><b><sup>1</sup>H NMR (300 MHz, CDCl</b><sub><b>3</b></sub><b>)</b> δ 9.68 (overlap, 2H), 8.03 (s, 1H), 7.38 (overlap, 2H), 6.97 (s, 1H), 6.54 (s, 1H), 6.28 (s, <i>1</i>H), 4.67 (s, 2H); <b><sup>13</sup>C NMR (75 MHz, CDCl</b><sub><b>3</b></sub><b>)</b> δ 179.3, 163.1, 148.8, 140.8, 131.0, 129.6, 129.13, 126.4, 122.8, 121.3, 115.5, 111.3, 110.1, 71.1; M<sup>+</sup> 345.9925.</p></div></div></div><div id="ml239.s15"><h2 id="_ml239_s15_">3. Results</h2><div id="ml239.s16"><h3>3.1. Dose Response Curves for Probe</h3><div id="ml239.f2" class="figure bk_fig"><div class="graphic"><a href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Figure%202.%20Dose-dependent%20Activity%20of%20the%20Probe%20(ML239)%20in%20Target%20and%20Counterscreen%20Assays.&p=BOOKS&id=133423_ml239f2.jpg" target="tileshopwindow" class="inline_block pmc_inline_block ts_canvas img_link" title="Click on image to zoom"><div class="ts_bar small" title="Click on image to zoom"></div><img src="/books/NBK133423/bin/ml239f2.jpg" alt="Figure 2. Dose-dependent Activity of the Probe (ML239) in Target and Counterscreen Assays." class="tileshop" title="Click on image to zoom" /></a></div><h3><span class="label">Figure 2</span><span class="title">Dose-dependent Activity of the Probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) in Target and Counterscreen Assays</span></h3><div class="caption"><p>Primary screen from dry powders on HMLE_sh_Ecad (IC<sub>50</sub> = 1.16 μM) (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493176" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493176</a>) (<i>A</i>); control cell line HMLE_sh_GFP (26.7 μM) Toxicity (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493196" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493196</a>) (<i>B</i>).</p></div></div></div><div id="ml239.s17"><h3>3.2. Cellular Activity</h3><p>The probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) clearly met the established probe criteria in whole cells specified for this project (<a class="figpopup" href="/books/NBK133423/table/ml239.t1/?report=objectonly" target="object" rid-figpopup="figml239t1" rid-ob="figobml239t1">Table 1</a>).</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figml239t1"><a href="/books/NBK133423/table/ml239.t1/?report=objectonly" target="object" title="Table 1" class="img_link icnblk_img figpopup" rid-figpopup="figml239t1" rid-ob="figobml239t1"><img class="small-thumb" src="/books/NBK133423/table/ml239.t1/?report=thumb" src-large="/books/NBK133423/table/ml239.t1/?report=previmg" alt="Table 1. Comparison of the Probe (ML239) to Project Criteria." /></a><div class="icnblk_cntnt"><h4 id="ml239.t1"><a href="/books/NBK133423/table/ml239.t1/?report=objectonly" target="object" rid-ob="figobml239t1">Table 1</a></h4><p class="float-caption no_bottom_margin">Comparison of the Probe (ML239) to Project Criteria. </p></div></div></div><div id="ml239.s18"><h3>3.3. Profiling Assays</h3><p>In order to gain insight into the possible mechanism that the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) could be targeting, gene expression studies were conducted. HMLE_sh_Ecad and HMLE_sh_GFP cells were treated with 1 μM (IC<sub>80</sub>) of the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) for 6 hours or 24 hours (Ecad6, Ecad24, GFP6, GFP24). In addition, a control sample was included where DMSO was added for 24 hours (Ecad0 and GFP0). cRNA synthesis from the total RNA samples passing Quality Control (QC) were analyzed on a Human HT-12 Expression BeadChip. One sample, Ecad0, failed QC controls, and this sample was discarded for analysis purposes. All remaining duplicate samples were normalized for subsequent comparison analysis.</p><p>Since at low expression levels the data appeared to have a nonlinear distribution between samples (data not shown), we chose to normalize using the Cubic Spline method. However, to ensure that this is sufficient for picking out significant genes of interest, we compared three additional normalization methods (Average, Quantile, and Rank Invariant) with Cubic Spline. All duplicate samples were normalized, and Ecad0 was compared with Ecad24 or GFP0. All genes displaying greater than a 2-fold difference in expression were compared in a Venn diagram for all normalization conditions. All methods provided overlapping gene sets of genes with greater than a 2-fold difference in expression. In all four methods of analysis, 34 genes and 428 genes were identified when comparing Ecad0 versus Ecad24 or Ecad0 versus GFP0, respectively Therefore, those overlapping genes were prioritized as genes of interest.</p><p>After normalization, genes that had greater than a 2-fold expression were compared: Ecad0 versus Ecad24 (<a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3A</a>)<b>,</b> Ecad0 versus GFP0 <b>(</b><a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3B</a>)<b>,</b> or GFP0 versus GFP24 (<a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3C</a>). Using Cubic Spline normalization, 54 genes were differentially regulated when comparing the control HMLE_sh_Ecad sample (Ecad0) with 24 hours of treatment with the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>; Ecad24). The majority of the genes that were altered only displayed differences at the 24-hour time point; however, some changes in gene expression were also observed at 6 hours (Ecad0) such as DNAJB9, NT5E, and KCTD12 (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3A</a>). These genes were largely not affected in the GFP samples after treatment with the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3A</a>).</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figml239f3" co-legend-rid="figlgndml239f3"><a href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" title="Figure 3" class="img_link icnblk_img figpopup" rid-figpopup="figml239f3" rid-ob="figobml239f3"><img class="small-thumb" src="/books/NBK133423/bin/ml239f3.gif" src-large="/books/NBK133423/bin/ml239f3.jpg" alt="Figure 3. Heat Map Comparisons of Differential Gene Expression." /></a><div class="icnblk_cntnt" id="figlgndml239f3"><h4 id="ml239.f3"><a href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-ob="figobml239f3">Figure 3</a></h4><p class="float-caption no_bottom_margin">Heat Map Comparisons of Differential Gene Expression. Genes that displayed greater than a 2-fold difference in expression were identified and plotted in a heat map, and the gene expression in all six conditions was compared. Ecad0 versus Ecad24 (<i>A</i>), Ecad0 <a href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-ob="figobml239f3">(more...)</a></p></div></div><p>Relatively few genes were altered as compared with the number of genes that differed when comparing the cell lines HMLE_sh_Ecad versus HMLE_sh_GFP. When comparing Ecad0 versus GFP0, 717 genes were differentially expressed (<a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3B</a>). This finding strongly supports the distinct phenotype of these two cell lines.</p><p>When comparing treatment with the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) in the HMLE_sh_GFP cell line (GFP0 versus GFP24), only five genes were identified as being differentially expressed (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3C</a>). Only one gene (PPDPF) overlapped in the gene sets identified when comparing the two cell lines (Ecad0 versus Ecad24 and GFP0 versus GFP24) (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3A</a>, <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3C</a>). Interestingly, the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) had differential effects on PPDPF in the HMLE_sh_Ecad and HMLE_sh_GFP cell lines. After treatment with the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>), PPDPF increased expression in the HMLE_sh_Ecad cell line whereas PPDPF decreased expression in the HMLE_sh_GFP control cell line (see <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3A</a>, <a class="figpopup" href="/books/NBK133423/figure/ml239.f3/?report=objectonly" target="object" rid-figpopup="figml239f3" rid-ob="figobml239f3">Figure 3B</a>). This data supports the previous primary and secondary assay data analyzing the effects of the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) and suggests that the probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) has few effects in the HMLE_sh_GFP cell line, and is highly selective for HMLE_sh_Ecad cell line.</p></div></div><div id="ml239.s19"><h2 id="_ml239_s19_">4. Discussion</h2><div id="ml239.s20"><h3>4.1. Comparison to Existing Art and How the New Probe is an Improvement</h3><p>The current state of the art for probe molecule salinomycin exhibits a potency of about 1 μM against breast CSCs (HMLE_sh_ECAD) (<a class="figpopup" href="/books/NBK133423/figure/ml239.f2/?report=objectonly" target="object" rid-figpopup="figml239f2" rid-ob="figobml239f2">Figure 2</a>); however, it should be noted that salinomycin shows toxicity against the control cell line (HMLE_sh_GFP) at 10 mM (<a class="figpopup" href="/books/NBK133423/figure/ml239.f2/?report=objectonly" target="object" rid-figpopup="figml239f2" rid-ob="figobml239f2">Figure 2</a>). Furthermore BiPDeC had difficulty repeating the selectivity seen previously (data not shown), which may be due to the less tractable nature of Salinomycin. In addition, Salinomycin is a known potassium ionophore (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>), which may cause toxicity to cell types not tested in this assay.</p><p>The new probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) exhibits a similar potency at 1.18 μM, however, a
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head to head comparison with Salinomycin shows this probe is more selective against the shEcad cell line and the Twist cell line displaying minimal toxicity up to 30 μM. The probe is also more attractive structurally allowing for rapid analog synthesis. In the investigation of prior art relevant to the breast cancer stem cell project, the following databases were used: SciFinder, Entrez, PubMed, PubChem, PatentLens. The search strings used and the hits found are seen in <a class="figpopup" href="/books/NBK133423/table/ml239.t2/?report=objectonly" target="object" rid-figpopup="figml239t2" rid-ob="figobml239t2">Table 2</a>. For all relevant references, the publications were analyzed and the findings are summarized (see <a class="figpopup" href="/books/NBK133423/table/ml239.t2/?report=objectonly" target="object" rid-figpopup="figml239t2" rid-ob="figobml239t2">Table 2</a>). The searches were performed on, and are current as of, April 11, 2011.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figml239t2"><a href="/books/NBK133423/table/ml239.t2/?report=objectonly" target="object" title="Table 2" class="img_link icnblk_img figpopup" rid-figpopup="figml239t2" rid-ob="figobml239t2"><img class="small-thumb" src="/books/NBK133423/table/ml239.t2/?report=thumb" src-large="/books/NBK133423/table/ml239.t2/?report=previmg" alt="Table 2. Search Strings and Databases Employed in the Prior Art Search." /></a><div class="icnblk_cntnt"><h4 id="ml239.t2"><a href="/books/NBK133423/table/ml239.t2/?report=objectonly" target="object" rid-ob="figobml239t2">Table 2</a></h4><p class="float-caption no_bottom_margin">Search Strings and Databases Employed in the Prior Art Search. </p></div></div><p>Literature and patent searches revealed nine small molecules capable of selectively inhibiting breast CSCs (<a class="figpopup" href="/books/NBK133423/figure/ml239.f4/?report=objectonly" target="object" rid-figpopup="figml239f4" rid-ob="figobml239f4">Figure 4</a>). It is important to note that salinomycin is the only small molecule shown to be effective in the cell line HMLE_sh_Ecad used in the primary assay. The effectiveness of salinomycin in HMLE_sh_Ecad cells was determined by the project provider, Eric Lander and co-workers, in which they developed an HTS screen to discover compounds that were selectively toxic for breast CSCs. Salinomycin was shown to provide a reduction in the proportion of CSCs with an IC<sub>50</sub> value of approximately 1 μM against HMLE_sh_Ecad with approximately 10-fold selectivity over the control HMLE_sh_GFP (<a class="bibr" href="#ml239.r7" rid="ml239.r7">7</a>). In addition, <i>ex vivo</i> and <i>in vivo</i> treatment of mice with intraperitoneal injection of salinomycin inhibited mammary tumor growth and increased differentiation of epithelial tumor cells. To date, this is the only report of active compounds against the HMLE_sh_Ecad cell line.</p><div class="iconblock whole_rhythm clearfix ten_col fig" id="figml239f4" co-legend-rid="figlgndml239f4"><a href="/books/NBK133423/figure/ml239.f4/?report=objectonly" target="object" title="Figure 4" class="img_link icnblk_img figpopup" rid-figpopup="figml239f4" rid-ob="figobml239f4"><img class="small-thumb" src="/books/NBK133423/bin/ml239f4.gif" src-large="/books/NBK133423/bin/ml239f4.jpg" alt="Figure 4. Known Small Molecules Inhibitors of Breast Cancer Stem Cells." /></a><div class="icnblk_cntnt" id="figlgndml239f4"><h4 id="ml239.f4"><a href="/books/NBK133423/figure/ml239.f4/?report=objectonly" target="object" rid-ob="figobml239f4">Figure 4</a></h4><p class="float-caption no_bottom_margin">Known Small Molecules Inhibitors of Breast Cancer Stem Cells. </p></div></div><p>There has been a recent increase in the research of selective killing of breast CSCs. Though interesting, the cells used in this report are not susceptible to these agents. In one approach, researchers targeted the breast CSC pathways involved in self-renewal and survival. These pathways include NF-KB, Notch, Hedgehog, and Wnt. The NF-KB inhibitors parthenolide and 8-quinolinol (8Q) were reported by Zhou et al. to inhibit breast CSC-dependent MCF7 sphere cell growth selectively over bulk MCF7 cell growth (<a class="bibr" href="#ml239.r10" rid="ml239.r10">10</a>). They reported that parthenolide and pyrrolidinedithiocarbamate inhibited sphere MCF7 cell growth by 33% and 51%, respectively, and showed no obvious growth inhibition of bulk MCF7 cells. This work was followed by a 2009 publication, in which Zhou et al. reported that 8Q inhibited the sphere cell proliferation by 86% at 5 μM and inhibited the bulk cells by 30% (<a class="bibr" href="#ml239.r11" rid="ml239.r11">11</a>). 8Q also showed some antitumor activity in both MCF7 and MDAMB-435 (breast cancer cell line) xenograft models, but it had a much better effect when combined with paclitaxel than either agent administered alone. Kakarala et al. reported that curcumin and piperine, respectively, inhibited Wnt signaling, ALDH+ cells (breast CSC biomarker) and mammosphere formation by 50% at 5 μM and completely at 10 μM (<a class="bibr" href="#ml239.r12" rid="ml239.r12">12</a>). In 2010, Li et al. showed that sulforaphane down-regulated the Wnt-pathway and could inhibit ALDH+ cells <i>in vitro</i> by 65–80% at 1–5 μM, but had minimal effect on the population of bulk breast cancer cell lines. In addition, sulforaphane inhibited mammosphere formation and the cancer cells from sulforaphane-treated mice failed to produce any tumors in recipient mice up to 33 days after implantations (<a class="bibr" href="#ml239.r13" rid="ml239.r13">13</a>).</p><p>Metformin, a known oral hypoglycemic agent, was reported to selectively kill breast CSCs through an unknown mechanism. In this study, the combination of metformin and doxorubicin had a synergistic effect in reducing tumor mass and preventing relapse in xenograft mice (<a class="bibr" href="#ml239.r14" rid="ml239.r14">14</a>). In addition, Jiralerspong et al. reported a study of 2529 patients undergoing neoadjuvant chemotherapy, in which the pathologic complete response rate following surgery was 24% for diabetic patients taking metformin, 8% for non-metformin diabetic patients, and 16% for nondiabetic patients (<a class="bibr" href="#ml239.r15" rid="ml239.r15">15</a>). Furthermore, using both CXCR1-blocking antibodies and the small molecule inhibitor, repertaxin, respectively, demonstrated that CXCR1 selectively decreased breast CSCs <i>in vitro</i> and in NOD/SCID xenograft models (<a class="bibr" href="#ml239.r16" rid="ml239.r16">16</a>).</p><p>Berberine was investigated to determine its effects on the enriched stem cell-like population of MCF-7 cells. After 72 hours, the viability of MCF-7 cells was reduced to 96%, 84%, 79%, 65%, and 56%, and the stem cell-like population was reduced to 1.4% (1.5% of MCF7 cells were the stem cell-like population cells), 1.1%, 0.9%, 0.5% and 0.2% by 10 nM, 100 nM, 1 μM, 10 μM, and 20 μM of berberine, respectively (<a class="bibr" href="#ml239.r17" rid="ml239.r17">17</a>).</p><p>All nine compounds identified through this project are registered with the NIH Molecular Libraries, and the respective compound information is provided in <a class="figpopup" href="/books/NBK133423/table/ml239.t3/?report=objectonly" target="object" rid-figpopup="figml239t3" rid-ob="figobml239t3">Table 3</a>.</p><div class="iconblock whole_rhythm clearfix ten_col table-wrap" id="figml239t3"><a href="/books/NBK133423/table/ml239.t3/?report=objectonly" target="object" title="Table 3" class="img_link icnblk_img figpopup" rid-figpopup="figml239t3" rid-ob="figobml239t3"><img class="small-thumb" src="/books/NBK133423/table/ml239.t3/?report=thumb" src-large="/books/NBK133423/table/ml239.t3/?report=previmg" alt="Table 3. Prior Art Substance Identifiers." /></a><div class="icnblk_cntnt"><h4 id="ml239.t3"><a href="/books/NBK133423/table/ml239.t3/?report=objectonly" target="object" rid-ob="figobml239t3">Table 3</a></h4><p class="float-caption no_bottom_margin">Prior Art Substance Identifiers. </p></div></div></div></div><div id="ml239.s21"><h2 id="_ml239_s21_">5. References</h2><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>1.</dt><dd><div class="bk_ref" id="ml239.r1">Bao S, Wu Q, McLendon RE, Hao Y, Shi Q, Hjelmeland AB, Dewhirst MW, Bigner DD, Rich JN. Glioma stem cells promote radioresistance by preferential activation of the DNA damage response. <span><span class="ref-journal">Nature. </span>2006 Dec 7;<span class="ref-vol">444</span>(7120):756–60.</span> Epub 2006 Oct 18. [<a href="https://pubmed.ncbi.nlm.nih.gov/17051156" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 17051156</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>2.</dt><dd><div class="bk_ref" id="ml239.r2">Diehn M, Cho RW, Lobo NA, Kalisky T, Dorie MJ, Kulp AN, Qian D, Lam JS, Ailles LE, Wong M, et al. Association
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of reactive oxygen species levels and radioresistance in cancer stem
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cells. <span><span class="ref-journal">Nature. </span>2009 Apr 9;<span class="ref-vol">458</span>(7239):780–3.</span> [<a href="/pmc/articles/PMC2778612/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2778612</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/19194462" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 19194462</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>3.</dt><dd><div class="bk_ref" id="ml239.r3">Diehn M, Clarke MF. Cancer stem cells and radiotherapy: new insights into tumor radioresistance. <span><span class="ref-journal">J Natl Cancer Inst. </span>2006 Dec 20;<span class="ref-vol">98</span>(24):1755–7.</span> [<a href="https://pubmed.ncbi.nlm.nih.gov/17179471" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 17179471</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>4.</dt><dd><div class="bk_ref" id="ml239.r4">Eyler CE, Rich JN. Survival of the fittest: cancer stem cells in therapeutic resistance and angiogenesis. <span><span class="ref-journal">J Clin Oncol. </span>2008 Jun 10;<span class="ref-vol">26</span>(17):2839–45.</span> [<a href="/pmc/articles/PMC2739000/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2739000</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/18539962" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18539962</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>5.</dt><dd><div class="bk_ref" id="ml239.r5">Li X, Lewis MT, Huang J, Gutierrez C, Osborne CK, Wu MF, Hilsenbeck SG, Pavlick A, Zhang X, Chamness GC, et al. Intrinsic resistance of tumorigenic breast cancer cells to chemotherapy. <span><span class="ref-journal">J Natl Cancer Inst. </span>2008 May 7;<span class="ref-vol">100</span>(9):672–9.</span> Epub 2008 Apr 29. [<a href="https://pubmed.ncbi.nlm.nih.gov/18445819" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18445819</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>6.</dt><dd><div class="bk_ref" id="ml239.r6">Mani SA, Guo W, Liao MJ, Eaton EN, Ayyanan A, Zhou AY, Brooks M, Reinhard F, Zhang CC, Shipitsin M, et al. The epithelial-mesenchymal transition generates cells with properties of stem cells. <span><span class="ref-journal">Cell. </span>2008 May 16;<span class="ref-vol">133</span>(4):704–15.</span> [<a href="/pmc/articles/PMC2728032/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2728032</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/18485877" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18485877</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>7.</dt><dd><div class="bk_ref" id="ml239.r7">Gupta PB, Onder TT, Jiang G, Tao K, Kuperwasser C, Weinberg RA, Lander ES. Identification of selective inhibitors of cancer stem cells by high-throughput screening. <span><span class="ref-journal">Cell. </span>2009 Aug 21;<span class="ref-vol">138</span>(4):645–59.</span> Epub 2009 Aug 13. [<a href="/pmc/articles/PMC4892125/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC4892125</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/19682730" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 19682730</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>8.</dt><dd><div class="bk_ref" id="ml239.r8">Dontu G, Abdallah WM, Foley JM, Jackson KW, Clarke MF, Kawamura MJ, Wicha MS. In vitro propagation and transcriptional profiling of human mammary stem/progenitor cells. <span><span class="ref-journal">Genes Dev. </span>2003 May 15;<span class="ref-vol">17</span>(10):1253–70.</span> [<a href="/pmc/articles/PMC196056/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC196056</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/12756227" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 12756227</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>9.</dt><dd><div class="bk_ref" id="ml239.r9">Culig Z. Cytokine disbalance in common human cancers. <span><span class="ref-journal">Biochim Biophys Acta. </span>2011 1813 Feb;(2):308–14.</span> Epub 2010 Dec 15. [<a href="https://pubmed.ncbi.nlm.nih.gov/21167870" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 21167870</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>10.</dt><dd><div class="bk_ref" id="ml239.r10">Zhou J, Zhang H, Gu P, Bai J, Margolick JB, Zhang Y. NF-kappaB pathway inhibitors preferentially inhibit breast cancer stem-like cells. <span><span class="ref-journal">Breast Cancer Res Treat. </span>2008 Oct;<span class="ref-vol">111</span>(3):419–27.</span> Epub 2007 Oct 27. [<a href="/pmc/articles/PMC3320112/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC3320112</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/17965935" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 17965935</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>11.</dt><dd><div class="bk_ref" id="ml239.r11">Zhou J, Zhang H, Gu P, Margolick JB, Yin D, Zhang Y. Cancer stem/progenitor cell active compound 8-quinolinol in combination with paclitaxel achieves an improved cure of breast cancer in the mouse model. <span><span class="ref-journal">Breast Cancer Res Treat. </span>2009 May;<span class="ref-vol">115</span>(2):269–77.</span> Epub 2008 May 28. [<a href="/pmc/articles/PMC3320107/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC3320107</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/18506619" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18506619</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>12.</dt><dd><div class="bk_ref" id="ml239.r12">Kakarala M, Brenner DE, Korkaya H, Cheng C, Tazi K, Ginestier C, Liu S, Dontu G, Wicha MS. Targeting breast stem cells with the cancer preventive compounds curcumin and piperine. <span><span class="ref-journal">Breast Cancer Res Treat. </span>2010 Aug;<span class="ref-vol">122</span>(3):777–85.</span> Epub 2009 Nov 7. [<a href="/pmc/articles/PMC3039120/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC3039120</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/19898931" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 19898931</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>13.</dt><dd><div class="bk_ref" id="ml239.r13">Li Y, Zhang T, Korkaya H, Liu S, Lee HF, Newman B, Yu Y, Clouthier SG, Schwartz SJ, Wicha MS, Sun D. Sulforaphane, a dietary component of broccoli/broccoli sprouts, inhibits breast cancer stem cells. <span><span class="ref-journal">Clin Cancer Res. </span>2010 May 1;<span class="ref-vol">16</span>(9):2580–90.</span> Epub 2010 Apr 13. [<a href="/pmc/articles/PMC2862133/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2862133</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/20388854" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 20388854</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>14.</dt><dd><div class="bk_ref" id="ml239.r14">Hirsch HA, Iliopoulos D, Tsichlis PN, Struhl K. Metformin selectively targets cancer stem cells, and acts together with chemotherapy to block tumor growth and prolong remission. <span><span class="ref-journal">Cancer Res. </span>2009 Oct 1;<span class="ref-vol">69</span>(19):7507–11.</span> Epub 2009 Sep 14. [<a href="/pmc/articles/PMC2756324/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2756324</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/19752085" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 19752085</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>15.</dt><dd><div class="bk_ref" id="ml239.r15">Jiralerspong S, Palla SL, Giordano SH, Meric-Bernstam F, Liedtke C, Barnett CM, Hsu L, Hung MC, Hortobagyi GN, Gonzalez-Angulo AM. Metformin and pathologic complete responses to neoadjuvant chemotherapy in diabetic patients with breast cancer. <span><span class="ref-journal">J Clin Oncol. </span>2009 Jul 10;<span class="ref-vol">27</span>(20):3297–302.</span> Epub 2009 Jun 1. [<a href="/pmc/articles/PMC2736070/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2736070</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/19487376" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 19487376</span></a>]</div></dd></dl><dl class="bkr_refwrap"><dt>16.</dt><dd><div class="bk_ref" id="ml239.r16">Ginestier C, Liu S, Diebel ME, Korkaya H, Luo M, Brown M, Wicinski J, Cabaud O, Charafe-Jauffret E, Birnbaum D, et al. CXCR1 blockade selectively targets human breast cancer stem cells in vitro and in xenografts. <span><span class="ref-journal">J Clin Invest. </span>2010 Feb 1;<span class="ref-vol">120</span>(2):485–97.</span> Epub 2010 Jan 4. [<a href="/pmc/articles/PMC2810075/" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pmc">PMC free article<span class="bk_prnt">: PMC2810075</span></a>] [<a href="https://pubmed.ncbi.nlm.nih.gov/20051626" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 20051626</span></a>] [<a href="http://dx.crossref.org/10.1172/JCI39397" ref="pagearea=cite-ref&targetsite=external&targetcat=link&targettype=uri">CrossRef</a>]</div></dd></dl><dl class="bkr_refwrap"><dt>17.</dt><dd><div class="bk_ref" id="ml239.r17">Kim JB, Ko E, Han W, Shin I, Park SY, Noh DY. Berberine diminishes the side population and ABCG2 transporter expression in MCF-7 breast cancer cells. <span><span class="ref-journal">Planta Med. </span>2008 Nov;<span class="ref-vol">74</span>(14):1693–700.</span> Epub 2008 Oct 24. [<a href="https://pubmed.ncbi.nlm.nih.gov/18951337" ref="pagearea=cite-ref&targetsite=entrez&targetcat=link&targettype=pubmed">PubMed<span class="bk_prnt">: 18951337</span></a>]</div></dd></dl></dl></div><div style="display:none"><div style="display:none" id="figml239f2"><img alt="Image ml239f2" src-large="/books/NBK133423/bin/ml239f2.jpg" /></div></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK133423_pubdet_">Publication Details</h2><h3>Author Information and Affiliations</h3><p class="contrib-group"><h4>Authors</h4><span itemprop="author">Leigh Carmody</span>,<sup>1</sup><sup>,<a href="#ml239.fn1">*</a></sup> <span itemprop="author">Andrew Germain</span>,<sup>1</sup> <span itemprop="author">Barbara Morgan</span>,<sup>1</sup> <span itemprop="author">Lynn VerPlank</span>,<sup>1</sup> <span itemprop="author">Cristina Fernandez</span>,<sup>1</sup> <span itemprop="author">Erin Forbeck</span>,<sup>1</sup> <span itemprop="author">Amal Ting</span>,<sup>1</sup> <span itemprop="author">Yuxiong Feng</span>,<sup>2</sup> <span itemprop="author">Jose Perez</span>,<sup>1</sup> <span itemprop="author">Sivaraman Dandapani</span>,<sup>1</sup> <span itemprop="author">Benito Munoz</span>,<sup>1</sup> <span itemprop="author">Michelle Palmer</span>,<sup>1</sup> <span itemprop="author">Eric Lander</span>,<sup>1</sup> <span itemprop="author">Piyush B. Gupta</span>,<sup>1,2</sup> and <span itemprop="author">Stuart L. Schreiber</span><sup>1</sup>.<sup>*</sup></p><h4>Affiliations</h4><div class="affiliation"><sup>1</sup>
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The Broad Institute Probe Development Center, Cambridge, MA</div><div class="affiliation"><sup>2</sup>
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The Whitehead Institute, Cambridge, MA</div><div class="affiliation"><sup>*</sup> Corresponding author email:
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<a href="mailto:dev@null" data-email="gro.etutitsnidaorb@ydomracl" class="oemail">gro.etutitsnidaorb@ydomracl</a></div><h3>Publication History</h3><p class="small">Received: <span itemprop="datePublished">April 15, 2011</span>; Last Update: <span itemprop="dateModified">February 28, 2013</span>.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div></div><h3>Publisher</h3><p>National Center for Biotechnology Information (US), Bethesda (MD)</p><h3>NLM Citation</h3><p>Carmody L, Germain A, Morgan B, et al. Identification of a Selective Small-Molecule Inhibitor of Breast Cancer Stem Cells - Probe 1. 2011 Apr 15 [Updated 2013 Feb 28]. In: Probe Reports from the NIH Molecular Libraries Program [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2010-. <span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/mlprobe/ml243/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/mlprobe/ml227/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article><article data-type="fig" id="figobml239fu1"><div id="ml239.fu1" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK133423/bin/ml239fu1.jpg" alt="ML239." /></div><h3><span class="title"><a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a></span></h3></div></article><article data-type="table-wrap" id="figobml239tu1"><div id="ml239.tu1" class="table"><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK133423/table/ml239.tu1/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__ml239.tu1_lrgtbl__"><table><thead><tr><th id="hd_h_ml239.tu1_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">CID/ML No.</th><th id="hd_h_ml239.tu1_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Target Name</th><th id="hd_h_ml239.tu1_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">IC<sub>50</sub>/EC<sub>50</sub> (nM) [SID, AID]</th><th id="hd_h_ml239.tu1_1_1_1_4" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Anti-target</th><th id="hd_h_ml239.tu1_1_1_1_5" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">IC<sub>50</sub>/EC<sub>50</sub> (μM) [SID, AID]</th><th id="hd_h_ml239.tu1_1_1_1_6" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Fold Selective</th><th id="hd_h_ml239.tu1_1_1_1_7" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Secondary Assay(s)<br />IC<sub>50</sub>/EC<sub>50</sub> (nM) [SID, AID]</th></tr></thead><tbody><tr><td headers="hd_h_ml239.tu1_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">CID 49843203/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a></td><td headers="hd_h_ml239.tu1_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">Breast Cancer Stem Cell-like cell</td><td headers="hd_h_ml239.tu1_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">1180 (1.18 μM)<br />[<a href="https://pubchem.ncbi.nlm.nih.gov/substance/104170348" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">SID 104170348</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493226" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493226</a>]</td><td headers="hd_h_ml239.tu1_1_1_1_4" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">Mammary Epithelial Cell</td><td headers="hd_h_ml239.tu1_1_1_1_5" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">27.6<br />[<a href="https://pubchem.ncbi.nlm.nih.gov/substance/104170348" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">SID 104170348</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504325" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504325</a>]</td><td headers="hd_h_ml239.tu1_1_1_1_6" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">23.4-fold</td><td headers="hd_h_ml239.tu1_1_1_1_7" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">tumorsphere assay<br />No activity<br />[<a href="https://pubchem.ncbi.nlm.nih.gov/substance/114279607" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">SID 114279607</a>, <a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/504623" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 504623</a>]</td></tr></tbody></table></div></div></article><article data-type="fig" id="figobml239f1"><div id="ml239.f1" class="figure bk_fig"><div class="graphic"><a href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Figure%201.%20Stability%20Data%20for%20the%20Probe%20(CID%2049835877%2FML239)%20in%20PBS%20Plus%20Acetonitrile%20Over%2048%20Hours.&p=BOOKS&id=133423_ml239f1.jpg" target="tileshopwindow" class="inline_block pmc_inline_block ts_canvas img_link" title="Click on image to zoom"><div class="ts_bar small" title="Click on image to zoom"></div><img data-src="/books/NBK133423/bin/ml239f1.jpg" alt="Figure 1. Stability Data for the Probe (CID 49835877/ML239) in PBS Plus Acetonitrile Over 48 Hours." class="tileshop" title="Click on image to zoom" /></a></div><h3><span class="label">Figure 1</span><span class="title">Stability Data for the Probe (CID 49835877/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) in PBS Plus Acetonitrile Over 48 Hours</span></h3></div></article><article data-type="fig" id="figobml239f5"><div id="ml239.f5" class="figure bk_fig"><div class="graphic"><img data-src="/books/NBK133423/bin/ml239f5.jpg" alt="Scheme 1. Synthesis of the Probe (CID49843203/ML239)." /></div><h3><span class="label">Scheme 1</span><span class="title">Synthesis of the Probe (CID49843203/<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>)</span></h3></div></article><article data-type="fig" id="figobml239f2"><div id="ml239.f2" class="figure bk_fig"><div class="graphic"><a href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Figure%202.%20Dose-dependent%20Activity%20of%20the%20Probe%20(ML239)%20in%20Target%20and%20Counterscreen%20Assays.&p=BOOKS&id=133423_ml239f2.jpg" target="tileshopwindow" class="inline_block pmc_inline_block ts_canvas img_link" title="Click on image to zoom"><div class="ts_bar small" title="Click on image to zoom"></div><img data-src="/books/NBK133423/bin/ml239f2.jpg" alt="Figure 2. Dose-dependent Activity of the Probe (ML239) in Target and Counterscreen Assays." class="tileshop" title="Click on image to zoom" /></a></div><h3><span class="label">Figure 2</span><span class="title">Dose-dependent Activity of the Probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) in Target and Counterscreen Assays</span></h3><div class="caption"><p>Primary screen from dry powders on HMLE_sh_Ecad (IC<sub>50</sub> = 1.16 μM) (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493176" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493176</a>) (<i>A</i>); control cell line HMLE_sh_GFP (26.7 μM) Toxicity (<a href="https://pubchem.ncbi.nlm.nih.gov/bioassay/493196" ref="pagearea=body&targetsite=entrez&targetcat=link&targettype=pubchem">AID 493196</a>) (<i>B</i>).</p></div></div></article><article data-type="table-wrap" id="figobml239t1"><div id="ml239.t1" class="table"><h3><span class="label">Table 1</span><span class="title">Comparison of the Probe (<a href="/pcsubstance/?term=ML239[synonym]" ref="pagearea=body&targetsite=entrez&targetcat=term&targettype=pubchem">ML239</a>) to Project Criteria</span></h3><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK133423/table/ml239.t1/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__ml239.t1_lrgtbl__"><table class="no_top_margin"><thead><tr><th id="hd_h_ml239.t1_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:bottom;">No.</th><th id="hd_h_ml239.t1_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:bottom;">Property</th><th id="hd_h_ml239.t1_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:bottom;">Requirement</th><th id="hd_h_ml239.t1_1_1_1_4" rowspan="1" colspan="1" style="text-align:center;vertical-align:bottom;">Probe</th></tr></thead><tbody><tr><td headers="hd_h_ml239.t1_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">1</td><td headers="hd_h_ml239.t1_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Potency</td><td headers="hd_h_ml239.t1_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">10 μM</td><td headers="hd_h_ml239.t1_1_1_1_4" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">1.18 μM</td></tr><tr><td headers="hd_h_ml239.t1_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">2</td><td headers="hd_h_ml239.t1_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Selectivity</td><td headers="hd_h_ml239.t1_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">10-fold</td><td headers="hd_h_ml239.t1_1_1_1_4" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">26-fold</td></tr></tbody></table></div></div></article><article data-type="fig" id="figobml239f3"><div id="ml239.f3" class="figure bk_fig"><div class="graphic"><a href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Figure%203.%20Heat%20Map%20Comparisons%20of%20Differential%20Gene%20Expression.&p=BOOKS&id=133423_ml239f3.jpg" target="tileshopwindow" class="inline_block pmc_inline_block ts_canvas img_link" title="Click on image to zoom"><div class="ts_bar small" title="Click on image to zoom"></div><img data-src="/books/NBK133423/bin/ml239f3.jpg" alt="Figure 3. Heat Map Comparisons of Differential Gene Expression." class="tileshop" title="Click on image to zoom" /></a></div><h3><span class="label">Figure 3</span><span class="title">Heat Map Comparisons of Differential Gene Expression</span></h3><div class="caption"><p>Genes that displayed greater than a 2-fold difference in expression were identified and plotted in a heat map, and the gene expression in all six conditions was compared. Ecad0 versus Ecad24 (<i>A</i>), Ecad0 versus GFP 0 (<i>B</i>), GFP0 versus GFP24 (<i>C</i>).</p></div></div></article><article data-type="table-wrap" id="figobml239t2"><div id="ml239.t2" class="table"><h3><span class="label">Table 2</span><span class="title">Search Strings and Databases Employed in the Prior Art Search</span></h3><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK133423/table/ml239.t2/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__ml239.t2_lrgtbl__"><table class="no_top_margin"><thead><tr><th id="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Search String</th><th id="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Database</th><th id="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Hits Found</th></tr></thead><tbody><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“breast cancer stem cells”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Sci Finder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">328</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“breast cancer AND stem cells”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Patent Lens</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">1264</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“breast cancer stem cells”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Entrez<br />(PubChem Bioassay)</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">3151<br />(35)</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“salinomycin”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">1380</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“NF-Kβ inhibitors AND BCSC”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">18</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“Wnt inhibitors AND BCSC”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">27</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“CXCR inhibitors AND BCSC”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">7</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“Notch inhibitors AND BCSC”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">25</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“Hedgehog inhibitors AND BCSC”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">7</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“MCF7 AND stem cells”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Entrez<br />(PubChem Bioassay)</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">93<br />(5)</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“HMLE”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Entrez<br />(PubChem Bioassay)</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">7<br />(4)</td></tr><tr><td headers="hd_h_ml239.t2_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:middle;">“HMLE AND stem cells”</td><td headers="hd_h_ml239.t2_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">SciFinder</td><td headers="hd_h_ml239.t2_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">47</td></tr></tbody></table></div></div></article><article data-type="table-wrap" id="figobml239t3"><div id="ml239.t3" class="table"><h3><span class="label">Table 3</span><span class="title">Prior Art Substance Identifiers</span></h3><p class="large-table-link" style="display:none"><span class="right"><a href="/books/NBK133423/table/ml239.t3/?report=objectonly" target="object">View in own window</a></span></p><div class="large_tbl" id="__ml239.t3_lrgtbl__"><table class="no_top_margin"><thead><tr><th id="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">Compound Name</th><th id="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">CAS No.</th><th id="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:middle;">PubChem CID</th></tr></thead><tbody><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Repertaxin 266359</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">266359-83-5</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">9932389</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Parthenolide 20554</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">20554-84-1</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">5420804</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">8- Quinolinol</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">148-24-3</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">1923</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Sulforaphane</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">4478-93-7</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">9577379</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Metformin</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">657-24-9</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">4091</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Berberine</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">633-66-9</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">2353</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Salinomycin</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">53003-10-4</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">23682228</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Curcumin</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">458-37-7</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">969516</td></tr><tr><td headers="hd_h_ml239.t3_1_1_1_1" rowspan="1" colspan="1" style="text-align:left;vertical-align:top;">Piperine</td><td headers="hd_h_ml239.t3_1_1_1_2" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">94-62-2</td><td headers="hd_h_ml239.t3_1_1_1_3" rowspan="1" colspan="1" style="text-align:center;vertical-align:top;">638024</td></tr></tbody></table></div></div></article><article data-type="fig" id="figobml239f4"><div id="ml239.f4" class="figure bk_fig"><div class="graphic"><a href="/core/lw/2.0/html/tileshop_pmc/tileshop_pmc_inline.html?title=Figure%204.%20Known%20Small%20Molecules%20Inhibitors%20of%20Breast%20Cancer%20Stem%20Cells.&p=BOOKS&id=133423_ml239f4.jpg" target="tileshopwindow" class="inline_block pmc_inline_block ts_canvas img_link" title="Click on image to zoom"><div class="ts_bar small" title="Click on image to zoom"></div><img data-src="/books/NBK133423/bin/ml239f4.jpg" alt="Figure 4. Known Small Molecules Inhibitors of Breast Cancer Stem Cells." class="tileshop" title="Click on image to zoom" /></a></div><h3><span class="label">Figure 4</span><span class="title">Known Small Molecules Inhibitors of Breast Cancer Stem Cells</span></h3></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
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