Abstract
Structure-based modeling combined with rational drug design, and high throughput screening approaches offer significant potential for identifying and developing lead compounds with therapeutic potential. The present review focuses on these two approaches using explicit examples based on specific derivatives of Gossypol generated through rational design and applications of a cancer-specific-promoter derived from Progression Elevated Gene-3. The Gossypol derivative Sabutoclax (BI-97C1) displays potent anti-tumor activity against a diverse spectrum of human tumors. The model of the docked structure of Gossypol bound to Bcl-XL provided a virtual structure-activity-relationship where appropriate modifications were predicted on a rational basis. These structure-based studies led to the isolation of Sabutoclax, an optically pure isomer of Apogossypol displaying superior efficacy and reduced toxicity. These studies illustrate the power of combining structure-based modeling with rational design to predict appropriate derivatives of lead compounds to be empirically tested and evaluated for bioactivity. Another approach to cancer drug discovery utilizes a cancer-specific promoter as readouts of the transformed state. The promoter region of Progression Elevated Gene-3 is such a promoter with cancer-specific activity. The specificity of this promoter has been exploited as a means of constructing cancer terminator viruses that selectively kill cancer cells and as a systemic imaging modality that specifically visualizes in vivo cancer growth with no background from normal tissues. Screening of small molecule inhibitors that suppress the Progression Elevated Gene-3-promoter may provide relevant lead compounds for cancer therapy that can be combined with further structure-based approaches leading to the development of novel compounds for cancer therapy.
Keywords: Progression Elevated Gene-3, Sabutoclax, Apogossypol, BI-97C1, Gossypol, AP-1, PEA3, ETV4, E1AF, c-fos, c-jun, Cancer Terminator Virus
STRUCTURE-BASED APPROACHES FOR CANCER DRUG DISCOVERY
Cancer is a progressive disease characterized by sequential changes in gene expression mediated by both genetic and epigenetic alterations in the evolving tumor cell [1–3]. This intrinsic complexity and the heterogeneous nature of cancer, which is often further exacerbated during cancer expansion and progression to metastasis, has proven to be a significant impediment for developing effective therapies [3]. An inherent property of many cancer cells involves resistance to therapeutic agents that promote programmed cell death (apoptosis) in tumors, which is designed to limit growth and destroy tumors. [4]. Apoptosis plays a fundamental role in tissue homeostasis by ensuring a proper balance between cell loss and cell production. Defective regulation of apoptosis is implicated to various extents in virtually every malignancy [4]. Inhibition of apoptosis provides cancer cells with a selective growth advantage promoting survival and chemoresistance [5, 6]. The B-cell lymphoma/leukemia-2 (Bcl-2) family of proteins is a central regulator of apoptosis [7]. The Bcl-2 family of anti-apoptotic proteins comprise Bcl-2, Mcl-1, Bcl-XL, Bfl-1, Bcl-W and Bcl-B. The Bcl-2 protein family also includes pro-apoptotic effector proteins Bak, Bax, Bad, Bid, and Bim. The pro-apoptotic Bcl-2 family proteins heterodimerize with the anti-apoptotic proteins neutralizing their activity and inhibiting apoptosis [5]. Heterodimerization occurs through a hydrophobic crevice on the surface of the anti-apoptotic Bcl-2 family member and the α-helix BH3 domain of pro-apoptotic family members [7]. Because overexpression of Bcl-2 family members is prevalent in many types of cancer, they provide attractive targets for the development of novel therapeutics with anti-cancer properties. Molecules that mimic the BH3 domain of pro-apoptotic Bcl-2 members may effectively induce apoptosis and/or neutralize the ability of anti-apoptotic Bcl-2 family members to promote cancer cell survival [8–10].
A small library of natural products was screened using a combination of nuclear magnetic resonance (NMR)-based binding assays and fluorescence polarization displacement assays (FPA) identifying two polyphenols, Gossypol (NSC19048) and Purpurogallin, that could inhibit a BH3 peptide binding to BCLxL. Gossypol and Purpurogallin displace the BH3 peptide from binding Bcl-XL in the FPA assay with an IC50 of 0.5 μM and 2.2 μM, respectively [11]. Gossypol is a natural product derived from cotton seed extracts which was originally investigated as a male contraceptive agent in China [12]. Gossypol inhibits the growth of a diverse array of human breast, prostate, ovarian and pancreatic cancer cell lines and xenograft models [13–16]. Studies aimed at identifying the target of Gossypol suggested that this compound can induce apoptosis in cells overexpressing Bcl-2 or Bcl-XL [17]. Purpurogallin a less potent inhibitor of Bcl-XL is an anti-oxidant found in edible oils reported to inhibit tyrosine-specific protein kinase and DNA synthesis in glioblastoma cells [18, 19].
Mapping chemical-shift differences induced by Gossypol or Purpurogallin binding to 15N-labeled-Bcl-XL with heteronuclear NMR spectroscopy revealed that Gossypol binds more tightly than Purpurogallin to Bcl-XL, and that the binding of the polyphenols occurs most likely in the BH3 binding pocket of Bcl-XL. Docking studies using the Bcl-XL confirmation found in complex with Bax peptide revealed an optimal location for Gossypol binding in a deep hydrophobic cleft normally occupied by the Bak helical BH3 peptide domain. Furthermore, the docking studies showed that the (−) enantiomer of Gossypol binds more tightly than (+) enantiomer of Gossypol. Purpurogallin produced ambiguous results in the docking studies, however studying the inhibitory effect of Purpurogallin analogues allowed the identification of essential pharmacophoric sub-structures common to these polyphenols [11].
The (−) enantiomer of Gossypol (AT-101) is in clinical trials involving patients with solid tumors, lymphoma and leukemia. Although Gossypol is efficacious in cancer patients’ adverse events are associated with treatment including hepatocytotoxicity and gastrointestinal cytotoxicity. Since Gossypol is only a modest inhibitor of Bcl-XL it is likely that high doses of compound would be required for efficacy in patients, however dose limiting toxicity is apparent in the clinical trials. This issue generated a need to develop a structure-activity relationship (SAR) with Gossypol to identify more potent and selective inhibitors of Bcl-XL. The model of the docked structure of Gossypol into Bcl-XL also allowed for a virtual structure activity relationship where modifications of Gossypol were predicted on a rational basis leading to more potent and selective inhibitors [20]. We hypothesized that the reactive aldehyde residues in Gossypol were undesirable because they participate in Schiff’s base-type reactions, which may react with proteins and nucleic acids indiscriminately causing adverse side effects. We docked a small library of eight Gossypol derivatives modifying the aldehyde residues and found Apogossypol (1,1′,6,6′,7,7′-hexahydroxy-3,3′-dimethyl-5,5′-bis (1-methylethyl)-[2.2′-binaphthalene], NSC736630), a Gossypol derivative with the aldehyde residues eliminated having the lowest binding energy to Bcl-XL [20].
We compared the toxicity profile of Apogossypol and Gossypol to validate our hypothesis that the aldehyde residues contribute to adverse events of the compound. Both compounds are orally administrable, however single dose-pharmacokinetic studies revealed that Apogossypol has superior pharmacokinetic characteristics than Gossypol including greater blood concentrations over time (area under curve) due to reduced clearance of the compound [21, 22]. Mice tolerated two to four times higher doses of Apogossypol than Gossypol with less adverse events of hepatotoxicity and gastrointestinal toxicity in the group receiving Apogossypol. Accompanying reduced toxicity of Apogossypol was its superior efficacy in a model resembling human low-grade follicular lymphoma induced in transgenic mice by over-expression of Bcl-2 in B-cells [23]. B-cells from mice over-expressing Bcl-2 were more sensitive to cytotoxicity caused by in vitro Apogossypol treatment than Gossypol with LD50 values of 3 to 5 μM and 7.5 to 10 μM respectively [23]. Daily dosing of the maximum tolerated doses of these polyphenols illustrated that Apogossypol was superior to Gossypol in reducing splenomegaly and B-cell counts in spleens of Bcl-2 transgenic mice [23]. Taken together these results indicate that Apogossypol is a superior lead compound for anti-cancer therapy to the parent gossypol compound with increased activity and reduced adverse events.
Apogossypol is a racemic compound with the individual isomers of the compound being as effective in inhibiting Bcl-2 family members as the racemic mixture [24]. We synthesized 5, 5′ amide and ketone substituted Apogossypol derivatives and evaluated their activities and found compounds BI-79D10 and 8r with improved in vitro and in vivo efficacy compared to Apogossypol [24]. The structure of BI-97D10, 8r and the polyphenol parent compounds are illustrated in Fig. (1). Compound 8r is a mixture of diastereomers and has three centers of chirality. Because different enantiomers and diastereomers of compounds can have different physical, chemical and pharmacological properties as evident in the example presented above with Gossypol, we synthesized the four optically pure diastereomers of compound 8r and evaluated their activities. Of the four diastereomers, Sabutoclax (BI-97C1) was found to bind most tightly to BCLxL as we had done previously with NMR-spectroscopy. Sabutoclax inhibits binding of BH3 peptides to Bcl-XL, Bcl-2, Mcl-1, and Bfl-1 with IC50 values of 0.13, 0.56, and 0.049 μM respectively.
Concordant with the observation that Sabutoclax binds most tightly to Bcl-2 family members, it inhibits the growth of human prostate cancer and lung cancer and B-cell lymphoma lines with EC50 values of 0.13, 0.56, and 0.049 μM respectively [24]. Sabutoclax displays a 20-fold better efficacy in inhibiting the growth of PC-3 cells compared to BI-97D10. Furthermore, Sabutoclax show less cytotoxicity in bax/bak double-knockout cells compared to BI-97D10, suggesting that the mechanism of cell death provoked is dependent on Bcl-2 family members. Sabutoclax has superior in vivo efficacy compared to BI-97D10 in a transgenic mouse model of lymphoma where Bcl-2 is over-expressed in B-cells and in a human prostate cancer xenograft model dependent on Mcl-1 for growth [24]. Pharmacological inhibition of Mcl-1 expression with Sabutoclax, is sufficient to sensitize prostate tumors to mda-7/IL-24-induced apoptosis illustrating the power of combining an inhibitor Bcl-2 family proteins with a novel gene delivery modality [25, 26].
We have determined that Sabutoclax is a viable drug candidate due to the critical role of Bcl-2 family proteins in cancer progression, and this compound has been licensed to Oncothyreon Inc. for further development for human trials. From the initial discovery of polyphenols as inhibitors of Bcl-2 family proteins emerged Sabutoclax, a product of integration of structure-based modeling with rational design to predict derivatives of lead compounds to be empirically tested and evaluated for bioactivity.
UTILIZATION OF THE PEG-3-PROMOTER FOR CANCER IMAGING, GENE THERAPY AND DRUG DISCOVERY
Cancer is a progressive disease culminating in the acquisition of metastatic potential by a subset of evolving tumor cells [3]. Although extensively investigated resulting in significant progress in recent years, the precise molecular and biochemical events underlying tumor etiology in many cancers and cancer progression to metastasis remain ambiguous [1, 3]. Progression Elevated Gene-3 (PEG-3) was cloned by subtraction hybridization of cDNA libraries generated from E11, a mutant Ad5-(H5ts125)-transformed rat embryo cell clone that forms small, slow-growing, and compact tumors, and from an E11 isogenic clone developed from a highly aggressive tumorigenic nude mouse, E11-NMT (Fig. 2) [27–30]. The expression of PEG-3 directly correlates with cancer progression and acquisition of oncogenic potential by transformed rodent cells [30]. PEG-3 shares significant nucleotide and amino acid sequence homology with the hamster growth arrest and DNA damage-inducible gene gadd34 and a homologous murine gene, MyD116 that is induced during induction of terminal differentiation by interleukin-6 in murine myeloid leukemia cells [30]. The PEG-3 gene is a mutated and truncated form of gadd34/MyD116 that is commonly mutated in diverse rodent tumors and functions as a dominant-negative mutant of gadd34, promoting instead of inhibiting the cancer phenotype [31]. No similar mutation is observed in human cancers, but the promoter of rodent PEG-3 is selectively active in human cancer cells, as it is in rodent cancer cells [32–36]. The cancer specific activity of the minimal promoter region of PEG-3 has been demonstrated in human cancer cell lines of various tissues such as brain, prostate, breast and pancreas, as well as in metastatic melanoma (Fig. 3 and data not shown) [32–37]. The cancer-specific activity of the PEG-3-promoter is a versatile platform that we have used to successfully create cancer-imaging techniques (Figs. 4 and 5), conditionally replicating cancer terminator viruses (CTV) (Fig. 6), and a novel screening platform that identifies inhibitors of the transformed state as potential lead compounds with anti-cancer properties (Fig. 7).
PEG-3-promoter activity is regulated by Activating Protein-1 (AP-1) and PEA3/ETV4/E1AF transcription factors that are juxtaposed in the 512-bp region of the minimal PEG-3-promoter [38]. The PEA3 family of transcription factors comprises ETV5/ERM, ETV1/ER81 and PEA3. Elevated PEA3 expression correlates with poor prognosis in a broad array of clinical cancer samples from tissues including lung, stomach, liver, colon and others [39]. Many reports demonstrate the involvement of PEA3 in the transcriptional regulation of matrix metalloproteases (MMPs) involved with degradation of the extracellular matrix, a function required for cancer metastasis [40]. The AP-1 protein family is implicated in transformation and cell proliferation and has also been linked to apoptosis, differentiation, cellular migration, wound healing and inflammation [41–44]. AP1 and PEA3 are primarily regulated by the MAPKinase pathway, including extracellular related kinase (ERK), P38MAPK and SAPK/JNK cascades [45, 46]. There are also reports that link Rho/RACK or Wnt signaling pathway to PEA-3 leading to tumorigenesis [47]. A summary of the network of signaling pathways known to regulate AP-1 and PEA3 transcription are illustrated in Fig. (8). Juxtaposed AP-1 and PEA-3 binding sites are observed in genes that contribute to cancer progression including Her2-mediated activation of the COX2 promoter, expression of urokinase plasminogen activator, induction of pro-angiogenic factor IL-8, and more recently expression of Notch ligands [48–51].
Molecular genetic imaging enables the visualization and quantification of the activity of a variety of tumor-specific gene promoters. Because of the cancer specific activity exerted by the PEG-3-promoter we illustrated that the systemic delivery of a PEG-3-promoter-driven imaging construct can be used to visualize melanoma and breast cancer metastases in vivo with two distinct reporters (Figs. 4 and 5) [37]. Previous promoters utilized to visualize cancer in vivo were derived from human telomerase reverse transcriptase, survivin, and carcinoembryonic antigen that employed adenovirus delivery of the promoter for tumor-specific reporter expression [52–54]. Due to the use of adenoviral vectors for delivery, treatment was limited to local delivery with systemic delivery resulting in accumulation of the vector in the liver. The advantage of utilizing the PEG-3-promoter for tumor specific imaging is that it uses a non-viral vector allowing for systemic delivery of the vector. Since the PEG-3-promoter has a high level of constitutive activity it drives reporter genes at level detectable without the requirement of promoter amplification, a common requirement in other promoter-based imaging methods [37]. Further studies are required in other tumor types to determine if a wide variety of tumor types can be imaged with this methodology. Based on previous studies indicating the wide spectrum tumor-specific activity of the PEG-3-promoter [32–37], it is highly likely that this methodology will be applicable to a large number of additional tumor indications. The translational implications of this finding would not only aid tumor detection, but also extend to pre-operative planning, intraoperative management and therapeutic monitoring. Additionally, by combining this unique delivery methodology in combination with both an imaging and therapeutic agent, “theranostics”, it would be possible to both visualize the cancer and destroy it using a single reagent [55].
The cancer selectivity of the PEG-3-promoter has been utilized to successfully construct Cancer Terminator Viruses (CTVs), which successfully eradicate pancreatic, prostate and melanoma tumors (Fig. 6) [33–36]. Cancer-specific replication of the CTV occurs because the E1A gene, required for replication, is driven by the PEG-3 promoter. The CTV simultaneously expresses a second transgene in the E3 region that encodes an apoptosis-inducing or immunomodulatory cytokine, such as interferon (IFN-gamma) or melanoma differentiation associated gene-7/interleukin-24 (mda-7/IL-24) [33–36]. These CTVs then produces large quantities of the transgene protein as a function of adenovirus replication uniquely in cancer cells and eradicates the cancer. The advantages of using mda-7/IL-24 as the second transgene relate to both the direct and indirect anti-tumor effects of this cancer selective apoptosis- and toxic autophagy-inducing cytokine [56–71]. mda-7/IL-24: induces apoptosis or toxic autophagy in a broad spectrum of human cancers without affecting normal cells or tissues; inhibits tumor angiogenesis; is a potent anti-cancer immune modulatory agent; synergizes with current modalities of therapy including radiation, chemotherapy and antibody therapy; induces a potent ‘bystander’ anti-tumor effect as a secreted therapeutic cytokine; and has been shown to be safe, well tolerated and clinically efficacious in a Phase I clinical trial when injected intratumorally in patients with advanced cancers [56–77].
Since a major challenge of gene therapy is to develop an effective means to deliver toxic gene products we then set out to develop an alternative to delivering the CTVs intratumorally. We achieved this through engineering complexes of the CTV virus in Ultrasound (US) contrast agents (microbubbles), which would allow for targeted release through ultrasound following systemic injection of the CTV. This ultrasound-targeted microbubble-destruction (UTMD) approach involving US-guided CTV-microbubbles eradicated prostate cancer tumors in mice, not only in the targeted region, but also non-targeted sites distant from the primary tumor because of secondary viral infection and secreted mda-7/IL-24 [2, 78]. This approach has significant potential for therapeutic applications, since it has been used to successfully deliver a non-replicating tropism modified adenovirus (Ad.5/3-mda-7) into the prostate of Hi-Myc transgenic mice that develop pathogenic changes similar to humans developing prostate cancer [25]. When UTMD with Ad.5/3-mda-7 was combined with Sabutoclax (BI-97C1) in the Hi-Myc mice tumor growth and progression was abrogated [25]. These developments highlight the potential use of this novel image-guided viral gene therapy technology for use in patients with advanced metastatic disease.
Since the PEG-3-promoter provides a relevant unbiased (not based on the genetic change(s) causing the cancer) readout of the transformed state and cancer progression, compounds that inhibit PEG-Prom activity can potentially reverse the cancer phenotype. We have designed a screening paradigm to identify potential inhibitors of the transformed state utilizing the PEG-3-promoter as a primary screen. HeLa cells stably expressing a construct encoding the PEG-3-promoter driving luciferase expression (HeLa-PEG-luc) were screened with the full NIH Molecular Libraries Small Molecule Repository library consisting of >330,000 compounds to identify potential inhibitors of the PEG-3-promoter. A total of 6,143 compounds inhibited the PEG-3-promoter at least 50% and will be subjected to further counterscreens (Pubchem AID: 588405).
Hits from the primary high-throughput-screening (HTS) will be evaluated in a number of secondary assays (Fig. 7). We will determine if hits can inhibit the activity of the GAPDH-promoter driving luciferase expression stably in HeLa cells. Counter-screening with the GAPDH-promoter will allow us to discard general inhibitors of transcription/translation as well as discard compounds that can inhibit luciferase enzymatic activity. Furthermore, compound cytotoxicity will be determined to ensure promoter inhibition observed is not a consequence of generalized cellular cytotoxicity. A direct secondary screen will be developed in which the individual regions of the PEG-3-promoter that contain a functional or mutated AP-1 or PEA-3 site linked to a Luc reporter gene will be engineered into HeLa cells. These cells will be used to determine if specific compounds inhibit PEG-3-promoter function by blocking activity of AP-1 or PEA-3. Identified small molecule inhibitors could, in principle, exert their effects through any of these known pathways or through yet to be discovered pathways (Fig. 8). Our screening paradigm should permit a distinction and identification of the pathways through which any identified inhibitor may function.
We have developed a series of clones derived from CREF (Fischer cloned rat embryo fibroblast) cells [79] that are transformed morphologically and biologically (induce cells to grow anchorage independently and induce tumors in nude mice) by a single oncogene [30, 38, 79–84]. This series contains transformed CREF cells derived from transfection and overexpression of Ha-ras, v-raf, v-src, human papilloma virus type 18, AEG-1, type 5 adenovirus, c-Jun, high molecular weight DNA from human prostate cancer, etc. [79–84]. This panel of cells will permit us to define potential oncogene-regulated pathways modulated by specific small molecules identified in the HTS efforts. Confirmation of specific mode of action could also be ascertained by specifically extinguishing the function of defined oncogenes using known pharmacological or small molecule inhibitors of distinct oncogenic pathways, such as ras or src inhibitors, or by using siRNA approaches [84–86]. These studies will help elucidate potential mechanisms of action of chemical probes identified.
We conducted a pilot screen of ~14,400 compounds using the strategy described above and identified a PEG-3-promoter-inhibitor (unpublished data). This PEG-3-promoter inhibitor selectively kills human cancer cell lines derived from breast, prostate, pancreatic and brain with minimal cytotoxicity to untransformed counterpart cell lines. Treatment with the PEG-3-promoter-inhibitor suppresses PEA3 protein expression in cancer cell lines, which may be the event responsible for inhibiting the PEG-3-promoter. Since PEA3 associates with cancer progression this may also be a mechanism by which this PEG-3-promoter-inhibitor suppresses cancer growth. More follow up studies are required to delineate the target of this PEG-3-promoter-inhibitor, however this study suggests that this screening methodology is a viable strategy to produce lead compound with anti-cancer properties. Once targets of compounds are identified, structure-based modeling and rational design will be applied to yield second-generation compounds with superior anti-cancer activity. Furthermore, the use of the PEG-3-promoter as a systemic imaging agent as described earlier will allow us to determine if molecular probes identified using our HTS approaches can affect tumor expression of the PEG-3-promoter in vivo.
Acknowledgments
The present studies were supported in part by National Institutes of Health grants R03 MH093195, R01 CA097318 and P01 CA104177, and the National Foundation for Cancer Research (P.B.F.); the Samuel Waxman Cancer Research Foundation (D.S. and P.B.F.); USAMRAA W81XWH-10-PCRP-SIDA (P.B.F. and X.-Y.W.); USAMRAA, Army Prostate Cancer DoD Award W81XWH-11-1-0186 (S.S and P.B.F.); National Institutes of Health grant R01 CA149668 (J.C.R., M.P.) and California Institute for Regenerative Medicine grant TR2-01789 (M.P.); National Institutes of Health grants CA092871 and CA151838 (M.G.P.); National Institutes of Health Grant R01 CA138540 and Grants from the James S. McDonnell Foundation (D.S.).
ABBREVIATIONS
- AP-1
Activating Protein-1
- AS
Antisense
- BCL-2
B-cell lymphoma/leukemia-2
- CREF
Fischer cloned rat embryo fibroblast
- CTV
Cancer terminator viruses
- ERK
Extracellular related kinase
- FPA
Fluorescence polarization displacement assays
- GFP
Green fluorescent protein
- HTS
High throughput screening
- IFN
Interferon
- mda-7/IL-24
melanoma differentiation associated gene-7/interleukin-24
- MMP
Matrix metalloprotease
- NMR
Nuclear magnetic resonance
- PEG-3
Progression elevated gene-3
- SAR
Structure activity relationship
- US
Ultrasound
- UTMD
Ultrasound-targeted microbubble-destruction
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