Enabling Systemic Identification and Functionality Profiling for Cdc42 Homeostatic Modulators

Homeostatic modulation is pivotal in modern therapeutics. However, the discovery of bioactive materials to achieve this functionality is often random and unpredictive. Here, we enabled a systemic identification and functional classification of chemicals that elicit homeostatic modulation of signaling through Cdc42, a classical small GTPase of Ras superfamily. Rationally designed for high throughput screening, the capture of homeostatic modulators (HMs) along with molecular re-docking uncovered at least five functionally distinct classes of small molecules. This enabling led to partial agonists, hormetic agonists, bona fide activators and inhibitors, and ligand-enhanced agonists. Novel HMs exerted striking functionality in bradykinin-Cdc42 activation of actin remodelingand modified Alzheimer's disease-like behavior in mouse model. This concurrent computer-aided and experimentally empowered HM profiling highlights a model path for predicting HM landscape.

One Sentence Summary

With concurrent experimental biochemical profiling and in silico computer-aided drug discovery (CADD) analysis, this study enabled a systemic identification and holistic classification of Cdc42 homeostatic modulators (HMs) and demonstrated the power of CADD to predict HM classes that can mimic the pharmacological functionality of interests.

Introduction

Maintainingbody homeostasisis the ultimate keyto health. Thereare rich resources of bioactive materials for this functionality from both natural and synthetic chemical repertories including partial agonists (PAs) and various allosteric modulators. These homeostatic modulators (HMs) play a unique role in modern therapeutics for human diseases such as mental disorders and drug addiction. Buspirone, for example, acts as a PA for serotonin 5-HT 1A receptor but is an antagonist of the dopamine D 2 receptor. Such medical useto treat general anxietydisorders (GADs) has become one of the most-commonly prescribed medications. However, most HMs in current uses target membrane proteins and are often derived from random discoveries. HMs as therapeutics targeting cytoplasmic proteins are even more rare despite that they are in paramount needs (e. g. targeting Ras superfamily small GTPases).

Rationale

Cdc42, a classical member of small GTPases of Ras superfamily, regulates PI3K-AKT and Raf-MEK-ERK pathways and has been implicated in various neuropsychiatric and mental disorders as well as addictive diseases and cancer. We previously reported the high-throughput in-silico screening followed by biological characterization of novel small molecule modulators (SMMs) of Cdc42-intersectin (ITSN) protein-protein interactions (PPIs). Based on a serendipitously discovered SMM ZCL278 with PA profile as a model compound, we hypothesized that there are more varieties of such HMs of Cdc42 signaling, and the model HMs can be defined by their distinct Cdc42-ITSN binding mechanisms using computer-aided drug discovery (CADD) analysis. We further reasoned that molecular modeling coupled with experimental profiling can predict HM spectrum and thus open the door for the holistic identification and classification of multifunctional cytoplasmic target-dependent HMs as therapeutics.

Results

The originally discovered Cdc42 inhibitor ZCL278 displaying PA properties prompted the inquiry whether this finding represented a random encounter of PAs or whether biologically significant PAs can be widely present. The top ranked compounds were initially defined by structural fitness and binding scores to Cdc42. Because higher binding scores do not necessarily translate to higher functionality, we performed exhaustive experimentations with over 2,500 independent Cdc42-GEF (guanine nucleotide exchange factor) assays to profile the GTP loading activities on all 44 top ranked compounds derived from the SMM library. The N-MAR-GTP fluorophore-based Cdc42-GEF assay platform provided the first glimpse of the breadth of HMs. A spectrum of Cdc42 HMs was uncovered that can be categorized into five functionally distinct classes: Class I-partial competitive agonists, Class II-hormetic agonists, Class III- bona fide inhibitors (or inverse agonists), Class IV- bona fide activators or agonists, and Class V-ligand-enhanced agonists. Remarkably, model HMs such as ZCL278, ZCL279, and ZCL367 elicited striking biological functionality in bradykinin-Cdc42 activation of actin remodeling and modified Alzheimer's disease (AD)-like behavior in mouse model. Concurrently, we applied Schrödinger-enabled analyses to perform CADD predicted classification of Cdc42 HMs. We modified the classic molecular docking to instill a preferential binding pocket order (PBPO) of Cdc42-ITSN, which was based on the five binding pockets in interface of Cdc42-ITSN. We additionally applied a structure-based pharmacophore hypothesis generation for the model compounds. Then, using Schrödinger's Phase Shape, 3D ligand alignments assigned HMs to Class I, II, III, IV, and V compounds. In this HM library compounds, PBPO, matching pharmacophoric featuring, and shape alignment, all put ZCL993 in Class II compound category, which was confirmed in the Cdc42-GEF assay.

Conclusion

HMs can target diseased cells or tissues while minimizing impacts on tissues that are unaffected. Using Cdc42 HM model compounds as a steppingstone, GTPase activation-based screening of SMM library uncovered five functionally distinct Cdc42 HM classes among which novel efficacies towards alleviating dysregulated AD-like features in mice were identified. Furthermore, molecular re-docking of HM model compounds led to the concept of PBPO. The CADD analysis with PBPO revealed similar profile in a color-coded spectrum to these five distinct classes of Cdc42 HMs identified by biochemical functionality-based screening. The current study enabled a systemic identification and holistic classification of Cdc42 HMs and demonstrated the power of CADD to predict an HM category that can mimic the pharmacological functionality of interests. With artificial intelligence/machine learning (AI/ML) on the horizon to mirror experimental pharmacological discovery like AlphaFold for protein structure prediction, our study highlights a model path to actively capture and profile HMs in potentially any PPI landscape.

Graphic Abstract

Identification and functional classification of Cdc42 homeostatic modulators HMs

Using Cdc42 HM model compounds as reference, GTPase activation-based screening of compound libraries uncovered five functionally distinct Cdc42 HM classes. HMs showed novel efficacies towards alleviating dysregulated Alzheimer's disease (AD)-like behavioral and molecular deficits. In parallel, molecular re-docking of HM model compounds established their preferential binding pocket orders (PBPO). PBPO-based profiling (Red reflects the most, whereas green reflects the least, preferable binding pocket) revealed trends of similar pattern to the five classes from the functionality-based classification.

Pharmacological Modulators of Small GTPases of Rho Family in Neurodegenerative Diseases

Classical Rho GTPases, including RhoA, Rac1, and Cdc42, are members of the Ras small GTPase superfamily and play essential roles in a variety of cellular functions. Rho GTPase signaling can be turned on and off by specific GEFs and GAPs, respectively. These features empower Rho GTPases and their upstream and downstream modulators as targets for scientific research and therapeutic intervention. Specifically, significant therapeutic potential exists for targeting Rho GTPases in neurodegenerative diseases due to their widespread cellular activity and alterations in neural tissues. This study will explore the roles of Rho GTPases in neurodegenerative diseases with focus on the applications of pharmacological modulators in recent discoveries. There have been exciting developments of small molecules, nonsteroidal anti-inflammatory drugs (NSAIDs), and natural products and toxins for each classical Rho GTPase category. A brief overview of each category followed by examples in their applications will be provided. The literature on their roles in various diseases [e.g., Alzheimer's disease (AD), Parkinson's disease (PD), Amyotrophic lateral sclerosis (ALS), Frontotemporal dementia (FTD), and Multiple sclerosis (MS)] highlights the unique and broad implications targeting Rho GTPases for potential therapeutic intervention. Clearly, there is increasing knowledge of therapeutic promise from the discovery of pharmacological modulators of Rho GTPases for managing and treating these conditions. The progress is also accompanied by the recognition of complex Rho GTPase modulation where targeting its signaling can improve some aspects of pathogenesis while exacerbating others in the same disease model. Future directions should emphasize the importance of elucidating how different Rho GTPases work in concert and how they produce such widespread yet different cellular responses during neurodegenerative disease progression.

Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer progression

Only a small number of genes are bona fide oncogenes and tumor suppressors such as Ras, Myc, β-catenin, p53, and APC. However, targeting these cancer drivers frequently fail to demonstrate sustained cancer remission. Tumor heterogeneity and evolution contribute to cancer resistance and pose challenges for cancer therapy due to differential genomic rearrangement and expression driving distinct tumor responses to treatments. Here we report that intratumor heterogeneity of Wnt/β-catenin modulator δ-catenin controls individual cell behavior to promote cancer. The differential intratumor subcellular localization of δ-catenin mirrors its compartmentalization in prostate cancer xenograft cultures as result of mutation-rendered δ-catenin truncations. Wild-type and δ-catenin mutants displayed distinct protein interactomes that highlight rewiring of signal networks. Localization specific δ-catenin mutants influenced p120ctn-dependent Rho GTPase phosphorylation and shifted cells towards differential bFGF-responsive growth and motility, a known signal to bypass androgen receptor dependence. Mutant δ-catenin promoted Myc-induced prostate tumorigenesis while increasing bFGF-p38 MAP kinase signaling, β-catenin-HIF-1α expression, and the nuclear size. Therefore, intratumor δ-catenin heterogeneity originated from genetic remodeling promotes prostate cancer expansion towards androgen independent signaling, supporting a neomorphism model paradigm for targeting tumor progression.

Abstract 2904: Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer cell fate and behavior

Only a small number of genes are bona fide oncogenes and tumor suppressors such as Ras, Myc, p53 and PTEN. However, targeting these cancer drivers frequently fail to demonstrate sustained cancer remission. Tumor heterogeneity and evolution contribute to cancer resistance and pose challenges for cancer therapy due to differential gene expression profiles driving distinct tumor responses to treatments. Here we report that intratumor heterogeneity of Wnt/β-catenin/armadillo modulator δ-catenin controls individual cell behavior to promote cancer. The differential intratumor subcellular localization of δ-catenin mirrors its compartmentalization in prostate cancer xenograft cultures as a result of mutation-rendered δ-catenin truncations. Wildtype and δ-catenin mutants displayed non-overlapping protein interactomes that highlight rewiring of signal networks. Localization specific δ-catenin mutants influenced p120ctn-dependent Rho GTPase phosphorylation and shifted cells towards bFGF-responsive growth, a known signal to bypass androgen receptor dependence. Mutant δ-catenin promoted Myc-induced prostate tumorigenesis by increasing proliferation over apoptosis as well as β-catenin stabilization and HIF-1α expression. Therefore, intratumor δ-catenin heterogeneity by genetic remodeling promotes prostate cancer expansion towards androgen independence, supporting a neomorphism model paradigm for targeting tumor progression.

Citation Format: Mingchuan Li, Jongdee Nopparat, Jiao Zhang, Byron J. Aguilar, Yan-Hua Chen, Jie Du, Xin Ai, Yong Luo, Yongguang Jiang, Christi Boykin, Qun Lu. Intratumor δ-catenin heterogeneity driven by genomic rearrangement dictates growth factor dependent prostate cancer cell fate and behavior [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2904.

Therapeutic Effect of Y-27632 on Tumorigenesis and Cisplatin-Induced Peripheral Sensory Loss through RhoA-NF-κB

Chemotherapy-induced peripheral neuropathy (CIPN) is a major side effect of cancer therapy that frequently requires a reduction or cessation of treatments and negatively impacts the patient's quality of life. There is currently no effective means to prevent or treat CIPN. In this study, we developed and applied CIPN in an immunocompetent, syngeneic murine Lewis Lung Carcinoma (LLCab) model that enabled the elucidation of both tumor and host responses to cisplatin and treatments of Y-27632, a selective inhibitor of Rho kinase/p160^ROCK. Y-27632 not only preserved cisplatin's efficacy toward tumor suppression but also the combination treatment inhibited tumor cell proliferation and increased cellular apoptosis. By alleviating the cisplatin-induced loss of epidermal nerve fibers (ENFs), Y-27632 protected tumor-bearing mice from cisplatin-induced reduction of touch sensation. Furthermore, quantitative proteomic analysis revealed the striking cisplatin-induced dysregulation in cellular stress (inflammation, mitochondrial deficiency, DNA repair, etc.)-associated proteins. Y-27632 was able to reverse the changes of these proteins that are associated with Rho GTPase and NF-κB signaling network, and also decreased cisplatin-induced NF-κB hyperactivation in both footpad tissues and tumor. Therefore, Y-27632 is an effective adjuvant in tumor suppression and peripheral neuroprotection. These studies highlight the potential of targeting the RhoA-NF-κB axis as a combination therapy to treat CIPN. IMPLICATIONS: This study, for the first time, demonstrated the dual antineoplastic and neuroprotective effects of Rho kinase/p160^ROCK inhibition in a syngeneic immunocompetent tumor-bearing mouse model, opening the door for further clinical adjuvant development of RhoA-NF-κB axis to improve chemotherapeutic outcomes.

Abstract A35: Targeting Ras downstream to control motions: Rho GTPases

Ras activation is at the center of many signaling cascades that drive cell transformation and carcinogenesis. Strategies targeting inhibition of cellular functions of Ras can be multifaceted, from its upstream elements such as growth factors and integrin receptors to its remote downstream elements. Cell motility is one such major element that controls whether a cancer cell can be lethal to the human body. Without gaining cancer unique motile ability, a cancer cell's deadly impact of metastasis would be crippled and be eliminated through available anti-neoplastic approaches.

There has been important progress in the discovery of small molecule modulators targeting the control machinery of cell motions, notably Rho subfamily of small GTPases, which is part of the Ras superfamily proteins. The classical proteins of the Rho GTPases are RhoA, Rac1, and Cdc42, which control the cytoplasmic tension (RhoA), cellular crawling (Rac1), and cellular scouting (Cdc42), respectively. Because these proteins are essential for cancer cell motility, establishment of a toolbox for the molecular modulators of their functions would significantly enhance the development of potential therapeutics aimed at targeting these pathways. Over the past decade, chemical compounds targeting RhoA pathway (Y-27632: Nature, 1997) and Rac1 (NSC23766: PNAS, 2004) became available. Our recent identification of a small molecule modulating Cdc42 (ZCL278: PNAS, 2013) has provided a complete reservoir that could be used to explore their differential effects on cancer cell behavior.

ZCL278 and NSC23766 suppressed prostate cancer cell motility and they showed differential effects on cell survival. While ZCL278 did not decrease cell viability, NSC23766 did so in the same time frame. Our recent unpublished studies also found that they differentially influence cell cycle progression. Cells derived from different cancer types responded differently to Rac1 and Cdc42 modulation. Furthermore, cells derived from different individuals of the same cancer types responded differently, emphasizing the heterogeneity of potential drug responses of different cancers or same cancer types from different individuals. For example, in prostate cancer cells, ZCL278 increased S-phase block, resulting a diminished G2/M-phase in a dose-dependent manner whereas the effects of NSC23766 on G2/M reduction were not significant. In lung cancer cells, the effects of ZCL278 and NSC23776 on cell cycle were modified. NSC23766 did not increase apoptosis of some lung cancer cell types at all. Therefore, ZCL278 and NSC23766 can suppress cell motility, cell proliferation and cell survival differently in different cancers. Our studies will provide the first glimpse of the effects of ZCL278 and NSC23766 on 5 different cancer types including breast, colon, lung, pancreas, and prostate cancer. Understanding the mechanisms of the cancer heterogeneity and the incorporation of differentiating biomarkers would significantly increase the intended efficacy of cancer therapeutics targeting Ras and its downstream elements. Our studies are supported in part by NIH grants CA111891, CA165202, and HL085752.

Citation Format: Qun Lu, Christi Boykin, Huchen Zhou, Amy Friesland, Yan-Hua Chen. Targeting Ras downstream to control motions: Rho GTPases. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr A35. doi: 10.1158/1557-3125.RASONC14-A35

δ-Catenin, a Wnt/β-catenin modulator, reveals inducible mutagenesis promoting cancer cell survival adaptation and metabolic reprogramming

Mutations of Wnt/β-catenin signaling pathway has essential roles in development and cancer. Although β-catenin and adenomatous polyposis coli (APC) gene mutations are well established and are known to drive tumorigenesis, discoveries of mutations in other components of the pathway lagged, which hinders the understanding of cancer mechanisms. Here we report that δ-catenin (gene designation: CTNND2), a primarily neural member of the β-catenin superfamily that promotes canonical Wnt/β-catenin/LEF-1-mediated transcription, displays exonic mutations in human prostate cancer and promotes cancer cell survival adaptation and metabolic reprogramming. When overexpressed in cells derived from prostate tumor xenografts, δ-catenin gene invariably gives rise to mutations, leading to sequence disruptions predicting functional alterations. Ectopic δ-catenin gene integrating into host chromosomes is locus nonselective. δ-Catenin mutations promote tumor development in mouse prostate with probasin promoter (ARR2PB)-driven, prostate-specific expression of Myc oncogene, whereas mutant cells empower survival advantage upon overgrowth and glucose deprivation. Reprogramming energy utilization accompanies the downregulation of glucose transporter-1 and poly (ADP-ribose) polymerase cleavage while preserving tumor type 2 pyruvate kinase expression. δ-Catenin mutations increase β-catenin translocation to the nucleus and hypoxia-inducible factor 1α (HIF-1α) expression. Therefore, introducing δ-catenin mutations is an important milestone in prostate cancer metabolic adaptation by modulating β-catenin and HIF-1α signaling under glucose shortage to amplify its tumor-promoting potential.

Abstract 4531: Anticancer potential of curcurbitacin IIa trough STAT3/JAK2-independent, survivin and PARP mediated apoptosis and disruption of actin cytoskeleton

The medicinal plant Hemsleya amalils Diels has been used as a homeopathic treatment for various diseases in China for centuries and has recently been indicated as being effective in inhibiting cancer cell growth. To investigate the molecular mechanisms underlying the anti-cancer activity of Hemsleya family, we purified the active component curcurbitacin IIa. Curcurbitacin IIa inhibited cell growth, induced apoptosis in several cancer cell lines, and reduced tumor growth in vivo. Immunofluorescent light microscopy as well as time-lapse imaging demonstrated the remarkable clustering of filamentous actin and the increases in G2/M populations in cell cycle, indicating the disruption of mitosis as the potential mechanism of inducing apoptosis by curcurbitacin IIa. Flowcytometry confirmed increased cell death while western blots showed reduced phospho-histone H3 immunoreactivity, consistent with reduced mitosis. Cleavage of Poly (ADP-ribose) polymerase or PARP, immediate upstream of DNA breakdown as a result of caspase activation, was increased dramatically while AKT phosphorylation and the Inhibitor of Apoptosis Protein survivin expression were reduced. Prostate cancer cells stably transfected with oncoprotein δ-catenin in which survivin expression was increased showed reduced efficacy of curcurbitacin IIa to induce cell death. Combined with lack of its effects on STAT3/JAK2 phosphorylation, theses studies highlight curcurbitacin IIa as a new class of anti-cancer drugs in suppression of cancer cell expansion by disrupting the actin cytoskeleton and directing the cell to undergo apoptosis through inhibition of surviving, AKT, and PARP. Supported by Department of Defense (PC040569) and National Cancer Institute (CA111891).

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4531.

Exercise and the heart. Good, benign, or evil?

The risks and benefits of regular aerobic exercise have been studied extensively. Because of the potential risks, we believe that sedentary persons over age 40 who have cardiac risk factors, as well as patients with coronary artery disease (CAD), should have a complete physical examination and probably an exercise electrocardiogram before starting a vigorous exercise program. In general, however, regular exercise has proven to be extra-ordinarily safe and the theoretical and proven benefits appear to greatly outweigh the risks in most people, including those with CAD, those with severe left ventricular dysfunction, and the elderly.