Targeted Disruption of MycâMax Oncoprotein Complex by a Small

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Targeted disruption of Myc-Max oncoprotein complex by a small molecule Seung H Choi, Madhupriya Mahankali, Sang Jun Lee, Mitchell Hull, H. Michael Petrassi, Arnab K Chatterjee, Peter G Schultz, Katherine A. Jones, and Weijun Shen ACS Chem. Biol., Just Accepted Manuscript • DOI: 10.1021/acschembio.7b00799 • Publication Date (Web): 04 Oct 2017 Downloaded from http://pubs.acs.org on October 5, 2017

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Targeted disruption of MycMyc-Max oncoprotein complex by a small molmolecule Seung H. Choi†, #, Madhupriya Mahankali‡, #, Sang Jun Lee‡, #, Mitchell Hull‡, H. Michael Petrassi‡, Arnab K. Chatterjee‡, Peter G. Schultz‡, §, *, Katherine A. Jones†, * and Weijun Shen‡, * †Regulatory Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037 USA ‡California Institute for Biomedical Research, La Jolla, CA 92037, United States §Department of Chemistry, the Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA 92037, USA ABSTRACT: MYC plays important roles in cell cycle progression, cell growth, and stem cell self-renewal. Although dysregulation of MYC expression is a hallmark of human cancers, there is no MYC targeted therapy yet. Here, we report sAJM589, a novel small molecule MYC inhibitor, identified from a PCA-based high-throughput screen. sAJM589 potently disrupt the Myc-Max heterodimer in a dose-dependent manner with an IC50 of 1.8 ± 0.03 µM. sAJM589 preferentially inhibits transcription of MYC target genes in a Burkitt lymphoma cell model, P493-6. Genome-wide transcriptome analysis showed that sAJM589 treatment and MYC depletion induce similar gene expression profiles. Consistently, sAJM589 suppressed cellular proliferation in diverse MYCdependent cancer cell lines and anchorage independent growth of Raji cells. Disruption of the Myc-Max interaction by sAJM589 reduced Myc protein levels, possibly by promoting ubiquitination and degradation of Myc. Collectively, these results suggest that sAJM589 may be a basis for the development of potential inhibitors of MYC-dependent cell growth.

The proto-oncogene MYC (myelocytomatosis viral oncogene homolog) belongs to the basic helix-loop-helix leucine zipper (B-HLH-LZ) transcription factor family and plays a key role in cellular proliferation, differentiation and apoptosis 1. MYC expression is normally under tight control; its expression is transient and responsive to mitogen stimulation 2. However, MYC expression can be dysregulated as a result of chromosome translocations, gene amplifications, or increased protein stability from loss of ubiquitin E3 ligases 3-5. Indeed, in more than 70% of human malignancies including lymphomas, neuroblastomas, melanomas, breast, ovarian, prostate and liver cancers, MYC is overexpressed 6. In MYC dependent cancer models, brief inactivation of MYC can not only regress tumor, but also induce cell death upon reactivation of MYC 7, suggesting that drugs target MYC could impact a range of human cancers. Unfortunately, the development of such drugs has been a challenge, owing to the absence of a defined catalytic or regulatory site amenable to small molecule inhibition. A number of proteins that interact with Myc are essential for its oncogenic activity. One of them, Max (MYC Associated factor X), binds to Myc through its C-terminal B-HLH-LZ domain, leading to heterodimerization, binding to the E-box (CACGTG) for transcription activation 8. Because Myc-Max heterodimerization is essential for MYC-driven oncogenesis, disruption of the MycMax interaction represents an attractive approach for inhibiting MYC function. Even though the binding interface between Myc and Max is large and without any “hot spots”, several molecules (Mycmycins, Mycro1, 2 and 3, 10058-F4, 10074G5 and KJ-9) have been identified that disrupt the Myc-Max protein-protein interaction (PPI) and inhibit MYC-driven cellular proliferation 6, 9, 10. Nevertheless, most of these compounds suffer from low cellular potency, sub-optimum pharmacological properties and/or potential off-target effects. To

identify additional small molecules that inhibit the Myc-Max interaction we carried out a Protein-fragment Complementation Assay (PCA)-based HTS and herein report the discovery of the small molecule, sAJM589, that is a potent MYC-Max inhibitor.

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Figure 1. sAJM589 was identified as MYC inhibitor from a PCAbased screen. (A) A schematic illustration of the Myc-Max PCA and the chemical structures of sAJM589 and 10058-F4. Dose response effect of sAJM589 and 10058-F4 in the Myc-Max PCA (B) and proliferation of P493-6 cells (C). Lysates from Myc-Max GLuc cells were treated with compound for 3 h followed by measurement of luciferase activity. Viability of P493-6 cells was measured 48 h after treatment with compounds. (D) sAJM589 inhibits HSCs but not differentiated M0 macrophages (M0 MΦ). HSCs were isolated from mouse bone marrow and differentiated into M0 MΦ in the presence of mCSF. These cells were treated with sAJM589 for 48 h and viability was measured. (E) Dose response effect of sAJM589 and 10058-F4 on the proliferation of various leukemic cell lines. Proliferating cancer cells (Ramos, HL-60 and KG1a) were treated with sAJM589 and 10058-F4 for 48 h and viability was determined after DMSO normalization (n=3).

First, we developed a quantitative assay for direct measurement of the Myc-Max interaction in a mammalian cell-based system that is amenable to a high-throughput screen (HTS). In this assay, HEK293 cells were engineered to stably express both full-length Max and the B-HLH-LZ domain (residues 335-439 a.a) of cMyc, fused to split Guassia luciferase Gluc1 and Gluc2, respectively. This Myc-Max Protein-fragment Complementary Assay (PCA) assay quantitatively measures the heterodimerization of Myc and Max, which is proportional to the luciferase reporter activity (Figure 1A). After optimization and miniaturization to 1536-well format, we used the known MYC inhibitor, 10058-F4 (IC50 = ~ 50 µM), to validate the Myc-Max PCA in a HTS format (Figure S1A). Subsequently, a screen of a diverse library of ~ 400K drug-like molecules (at 20 µM concentration) was performed (with a robust Z score > 0.75). Initial hits were defined as more than a 30% reduction of the signal (with 100% reduction of the signal provided by the positive control, 100058-F4 at 100 µM), and confirmed in an eight-point dose response (Figure S1B). Amongst a set of confirmed hit compounds, sAJM589 showed 100% inhibition of the signal at the screening concentration (Figure S1C). Biochemically, sAJM589 inhibited Myc-Max PCA activity in dose-responsive manner with an IC50 = 1.8 ± 0.03 µM (Figure 1B), ~ 25-fold more potent than 10058-F4. Next, sAJM589 was tested for its anti-proliferative activity in a Burkitt lymphoma cell model, P493-6 cells. P493-6 cell is an engineered B-cell line that overexpresses MYC in the absence of tetracycline (Tet-Off), leading to robust cell proliferation; in the presence of tetracycline, MYC expression is stringently suppressed (Tet-On). This cell line is widely used for studies of MYC-dependent transcription 11. Consistent with its potency in the biochemical assay, sAJM589 inhibited cellular proliferation of P493-6 (Tet-Off) in a dose dependent fashion with an IC50 = 1.9 ± 0.06 µM (Figure 1C and S1A), whereas its IC50 is > 20 µM in the presence of tetracycline (Figure S2A), indicating that sAJM589 is selectively targeting MYC. To further demonstrate the selectivity of sAJM589 on MYC dependent cellular proliferation, we tested the effect of sAJM589 on undifferentiated hematopoietic stem cells (HSCs), in which active MYC function is required for cellular proliferation 12-14. sAJM589 showed a dose dependent effect on the viability of undifferentiated HSCs with an IC50 of 5.8 ± 1.56 µM (Figure 1F). In contrast, sAJM589 has no effect on resting M0 macrophages (M0 MΦ) whose proliferation is independent of MYC activity (Figure 1D). To further investigate the activity of

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sAJM589 in additional MYC expressing cancer cells, Ramos, HL-60 and KG1a cells were treated for 48 h with increasing concentrations of sAJM589. Similar to its effect on P493-6 cells, sAJM589 showed a dose dependent inhibition of proliferation with IC50s of 0.9 ± 0.12, 1.2 ± 0.09 and 0.8 ± 0.11 µM in Ramos, HL-60 and KG1a, respectively, in a dose dependent manner (Figure 1E and S2). Initial analog synthesis indicate sAJM589 has narrow structure activity relationship (SAR) with sAJM589 showing superior efficacy in both biochemical PCA and proliferation assay among its structural analogs derived from chemical optimization (Figure S3).

Figure 2. sAJM589 selectively disrupts the Myc-Max interaction. (A) Inhibition of the Myc-Max interaction by sAJM589 in immunoprecipitation assay. Myc-Max PCA cells were treated with sAJM589 at indicated concentrations for 16 h, followed by immunoprecipitation and immunoblot assays. (B) The Myc-Max interaction is inhibited in P493-6 cells in the presence of sAJM589. Immunoprecipitation was carried out after treatment with sAJM589 for 16 h. (C) sAJM589 selectively inhibits MycMax but not Max-Max PCA. Max-Max and Myc-Max PCAs were performed in the presence of sAJM589 and shown as percent of DMSO (n=3). (D) sAJM589 has no effect on disrupting the JunFos interaction. Jun-Fos PCA cells were assayed with sAJM589 as described in (A). (E) aAJM589 disrupts DNA-binding by MycMax. Effect of sAJM589 on E-box DNA binding by 2 µM monitored by EMSA. (F) Biolayer interferometry curves of sAJM589 in dose response in the presence of biotin-tagged Myc protein (403-437 a.a).

To further validate whether sAJM589 directly inhibits the Myc-Max PPI, a co-immunoprecipitation assay was performed in the Myc-Max PCA cells that stably express HA-MaxGLuc1 and FLAG-Myc-GLuc2. Upon sAJM589 treatment, an


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immunoblot assay showed a dose dependent reduction in the levels of FLAG-Myc-GLuc2 protein from the immunoprecipitated HA-Max-GLuc1 protein complex (Figure 2A). Furthermore, co-immunoprecipitation assays in P493-6 cells using Max-specific anti-sera consistently reduced Max-bound Myc levels upon treatment with of sAJM589 in dose response (Figure 2B). The Myc-Max PPI is mediated by the interaction of their respective leucine zipper (LZ) domains, which is a common feature of family members in the Myc/Max/Mad network 15 . To test whether sAJM589 affects other LZ interactions, we established a Max-Max split GLuc assay (Max-Max PCA) cell line. Encouragingly, sAJM589 showed no effects on the PCA activity from the Max-Max PCA (Figure 2C). Because Myc binds to Max through direct contact between their leucinezipper domains, a number of previously identified MYC inhibitors (i.e., IIA4B20 and IIA6B17) also are able to inhibit other members of B-HLH-LZ family, such as Jun and Fos 16. Using a Jun-Fos PCA cell line that expresses HA-Fos-GLuc1 and FLAG-Jun-GLuc2 in HEK293 cells, co-immunoprecipitation assays demonstrated that sAJM589 does not disrupt the dimerization of Jun-Fos (Figure 2D and S4). Furthermore, the effect of sAJM589 on the mRNA levels of MYC or MAX in P493-6 cells and Raji cells is minimal (Figure S5), demonstrating that the effect of sAJM589 is largely at the protein level. Indeed, sAJM589 shows direct binding to the LZ region of Myc protein in dose responsive manner, as indicated by the bilayer interferometry (BLI) curves obtained with Octet Red (Figure 2F). Finally, over 2 µM of sAJM589 completely disrupted Ebox DNA binding affinity by Myc-Max complex (Figure 2E), further suggesting that sAJM589 selectively influences the MYC transcription program regulated by MYC.

lines) is plotted against the set of genes ordered by sAJM589 treatment at the x-axis.

Thus, to investigate the effects of sAJM589 on MYCdependent transcription, expression of typical MYC target genes was measured in P493-6 cells upon sAJM589 treatment. mRNA levels of several well-known MYC target genes (CAD, ODC1, NOP56/58, NPM1, NOLC1 17) decreased upon treatment with tetracycline (0.05 µM) or sAJM589 in dosedependent manner, without change in expression of the nonMYC target genes MAX and GAPDH (Figure 3A). To further explore the genome-wide effects of sAJ589, total RNA sequencing was performed on sAJM589 and tetracycline treated P493-6 cells. Using a threshold of 2-fold change (-1 > Log2∆), sAJM589 treatment down-regulated the transcription of 565 genes while tetracycline treatment decreased the transcription of 697 genes with an overlap of 526 genes (Figure S6). This result shows that the genome-wide changes in transcription by sAJM589 treatment are highly correlated with tetracycline treatment (Figure 3B), indicating that sAJM589 treatment largely recapitulates the effects of MYC depletion.

Figure 4. sAJM589 inhibits anchorage independent growth of cancer cells. (A) 2 x 103 of Burkitt lymphoma, Raji cells were embedded in agarose-matrix media. sAJM589 was applied as shown in the experimental scheme (Figure S7). Colony formation at 3 weeks is quantified as the bar graph. (B) Dose response reduction of Myc protein in Raji cells. Cells were treated with sAJM589 at indicated concentrations for 24 h. Immunoblot of total lysate was performed using indicated antibodies with a loading control of GAPDH.

Figure 3. sAJM589 induces transcriptional changes matching the effect from MYC depletion. (A) qRT-PCR analysis in P493-6 cells showed inhibition of mRNA levels of MYC target genes by sAJM589. P493-6 cells treated with sAJM589 or tetracycline at the indicated concentrations for 24 h was subject for qRT-PCR (n=3). (B) Total RNA-sequencing analysis in P493-6 cells treated with sAJM589 or tetracycline. Each gene is plotted at x-axis in order of differential expression (Log2 fold change of RNA abundance) upon treatment with sAJM589 (red smooth line). Differential mRNA expression upon tetracycline treatment (blue spiky

Because elevated MYC expression is essential for anchorageindependent growth, a hallmark of MYC function in cancer cells, we assayed anchorage-independent colony formation using the Burkitt lymphoma Raji cell line, where MYC is overexpressed by t(8;14) chromosome translocation. Raji cells were embedded in agarose-based solid matrix media for 20 days and treated with sAJM589 at day 8, 10, 12 and 14 (Figure 4A). The growth of Raji cells in solid matrix was strongly inhibited by sAJM589 in dose response comparing to vehicle control (Figure 4B). Immunoblot analysis of Raji cells showed reduced Myc levels at 10 and 20 µM of sAJM589 treatment (Figure 4C). In conclusion, sAJM589 is not only a potent inhibitor of Myc-Max interaction but also has its biological effects on cellular proliferation and growth in multiple MYCdependent cancer cell lines. To understand the mechanism of action of sAJM589, we next assessed whether sAJM589 affects Myc protein levels by interfering the Myc-Max PPI. Immunoblot analysis in P493-6 cells reproducibly demonstrated that AJM589 specifically decreased Myc protein levels (Figure 5A). Since sAJM589 has



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no effect on MYC mRNA levels in these cell lines (Figure S4), it likely affects degradation of Myc protein. Myc protein is rapidly turned over, with a typical half-life of less than 20 min in normal cells. However, the half-life of Myc protein is frequently increased in most of cancer cells, resulting in an elevation in Myc levels and corresponding gain of function 5. To measure the half-life of Myc protein in the presence of sAJM589, P493-6 cells were treated with the compound, and de novo protein synthesis was blocked by cycloheximide (CHX). Immunoblot analysis of the remaining Myc protein at different time points showed that sAJM589 treatment reduced Myc protein half-life by approximately two-fold (Figure 5B and 5C). In contrast, sAJM589 has no effect on Max stability in the range of concentrations tested.

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(D) Ubiquitination of Myc is increased in the presence of sAJM589. P493-6 cells were treated with either sAJM589 (20 µM) and/or MG-132 for 12 h. Myc was immunoprecipitated and visualized by immunoblot. High-molecular weight complex above Myc (65 kDa) was probed with ubiquitin-specific antibody to measure ubiquitination of Myc protein. GAPDH was used as input control.

Because ubiquitination is known to target Myc for proteasome-mediated degradation 18, 19, it is possible that increased turn-over of Myc protein in the presence of sAJM589 is due to enhanced ubiquitination. Indeed, sAJM589 treatment promoted the accumulation of ubiquitin-conjugated Myc in P493-6 cells when the proteasome inhibitor MG-132 prevents proteasome-mediated protein degradation (Figure 5C, lane 4). These data support the notion that sAJM589 facilitates ubiquitination of Myc by inhibiting Max binding to Myc and freeing its C-terminal region for E3 ubiquitin ligase, which results in its destruction by the proteasome.

ASSOCIATED CONTENT AUTHOR INFORMATION # these authors contribute equally to this work Corresponding Authors Authors *Email: [email protected]; *Email: [email protected]; *Email: [email protected];

ACKNOWLEDGMENT We would like to thank J. Janes, H. Nguyen, M. Wogan and T. Nordan for technical assistance and helpful discussions. Figure 5. sAJM589 triggers instability of Myc. (A) sAJM589 reduces Myc protein. Immunoblot analysis is shown from P493-6 cells treated with sAJM589 at the indicated concentrations for 24h. (B) sAJM589 facilitates turn-over of Myc. P493-6 cells were pre-incubated with either DMSO or sAJM589 (20 µM, 12 h), followed by CHX treatment to block de novo protein synthesis for up to 160 min. Myc was probed in the lysates with Max as a control. (C) Remaining levels of Myc protein are plotted in the graph. REFERENCES

1. Dang, C. V. (2012) MYC on the path to cancer, Cell 149, 2235. 2. Meyer, N., and Penn, L. Z. (2008) Reflecting on 25 years with MYC, Nat Rev Cancer 8, 976-990. 3. Keath, E. J., Caimi, P. G., and Cole, M. D. (1984) Fibroblast lines expressing activated c-myc oncogenes are tumorigenic in nude mice and syngeneic animals, Cell 39, 339-348. 4. O'Neil, J., Grim, J., Strack, P., Rao, S., Tibbitts, D., Winter, C., Hardwick, J., Welcker, M., Meijerink, J. P., Pieters, R., Draetta, G., Sears, R., Clurman, B. E., and Look, A. T. (2007) FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to gamma-secretase inhibitors, J Exp Med 204, 1813-1824.

SUPPORTING INFORMATION The Supporting Information, including Supplementary Figures S1-S7, Experimental Procedures and RNA_Seq data, is available free of charge on the ACS Publications at http://pubs.acs.org.

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