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.

Crosstalk between the Rho and Rab family of small GTPases in neurodegenerative disorders

Neurodegeneration is associated with defects in cytoskeletal dynamics and dysfunctions of the vesicular trafficking and sorting systems. In the last few decades, studies have demonstrated that the key regulators of cytoskeletal dynamics are proteins from the Rho family GTPases, meanwhile, the central hub for vesicle sorting and transport between target membranes is the Rab family of GTPases. In this regard, the role of Rho and Rab GTPases in the induction and maintenance of distinct functional and morphological neuronal domains (such as dendrites and axons) has been extensively studied. Several members belonging to these two families of proteins have been associated with many neurodegenerative disorders ranging from dementia to motor neuron degeneration. In this analysis, we attempt to present a brief review of the potential crosstalk between the Rab and Rho family members in neurodegenerative pathologies such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington disease, and amyotrophic lateral sclerosis (ALS).

RhoA-LIMK Signaling Axis Reveals Rostral-Caudal Plane and Spatial Dysregulation in the Brain of Alzheimer's Disease Mouse Models

BACKGROUND

RhoA signaling is widely reported to be dysregulated in Alzheimer's disease (AD), but its therapeutic targeting demonstrated mixed outcomes. We hypothesize that the activation and inactivation states of RhoA and LIMK are different in the cortex and in subregions of hippocampus along the rostral-caudal dimensions.

OBJECTIVE

We intended to elucidate the plane and spatial dependent RhoA signaling in association with AD.

METHODS

We applied antibody pRhoA that recognizes an inactive state of RhoA (S188 phosphorylation) and antibody pLIMK against an active state of LIMK (T508 phosphorylation) to investigate RhoA signaling in wildtype (WT) and triple transgenic AD (3xTg-AD) mouse model. We prepared serial sections from the rostral to caudal coronal planes of the entire mouse brain followed by immunofluorescence staining with pRhoA and pLIMK antibodies.

RESULTS

Both pRhoA and pLIMK elicited a shift of expression pattern from rostral to caudal planes. Additionally, pRhoA demonstrated dynamic redistribution between the nucleus and cytoplasm. pLIMK did not show such nucleus and cytoplasm redistribution but the expression level was changed from rostral to caudal planes. At some planes, pRhoA showed an increasing trend in expression in the cortex but a decreasing trend in the dentate gyrus of the 3xTg-AD mouse hippocampus. pLIMK tends to decrease in the cortex but increase in the dentate gyrus of 3xTg-AD mouse hippocampus.

CONCLUSIONS

RhoA activation is dysregulated in both human and mouse AD brains, and the RhoA-LIMK signaling axis reveals spatial dysregulation along the rostral-caudal plane dimensions.

Can GPR4 Be a Potential Therapeutic Target for COVID-19?

Coronavirus disease 19 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), first emerged in late 2019 and has since rapidly become a global pandemic. SARS-CoV-2 infection causes damages to the lung and other organs. The clinical manifestations of COVID-19 range widely from asymptomatic infection, mild respiratory illness to severe pneumonia with respiratory failure and death. Autopsy studies demonstrate that diffuse alveolar damage, inflammatory cell infiltration, edema, proteinaceous exudates, and vascular thromboembolism in the lung as well as extrapulmonary injuries in other organs represent key pathological findings. Herein, we hypothesize that GPR4 plays an integral role in COVID-19 pathophysiology and is a potential therapeutic target for the treatment of COVID-19. GPR4 is a pro-inflammatory G protein-coupled receptor (GPCR) highly expressed in vascular endothelial cells and serves as a "gatekeeper" to regulate endothelium-blood cell interaction and leukocyte infiltration. GPR4 also regulates vascular permeability and tissue edema under inflammatory conditions. Therefore, we hypothesize that GPR4 antagonism can potentially be exploited to mitigate the hyper-inflammatory response, vessel hyper-permeability, pulmonary edema, exudate formation, vascular thromboembolism and tissue injury associated with COVID-19.

The Proton-Sensing GPR4 Receptor Regulates Paracellular Gap Formation and Permeability of Vascular Endothelial Cells

GPR4 is a pH-sensing G protein-coupled receptor highly expressed in vascular endothelial cells and can be activated by protons in the inflamed tissue microenvironment. Herein, we report that acidosis-induced GPR4 activation increases paracellular gap formation and permeability of vascular endothelial cells through the G_α12/13/Rho GTPase signaling pathway. Evaluation of GPR4 in the inflammatory response using the acute hindlimb ischemia-reperfusion mouse model revealed that GPR4 mediates tissue edema, inflammatory exudate formation, endothelial adhesion molecule expression, and leukocyte infiltration in the inflamed tissue. Genetic knockout and pharmacologic inhibition of GPR4 alleviate tissue inflammation. These results suggest GPR4 is a pro-inflammatory receptor and could be targeted for therapeutic intervention.

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Acidosis/GPR4 regulates endothelial paracellular gap formation and permeability

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GPR4 exacerbates inflammation by increasing tissue edema and leukocyte infiltration

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Pharmacological inhibition of GPR4 reduces inflammatory responses

Clinical guidelines for management of patients under Lieutenant Governor's Warrants

This paper examines three categories of mentally abnormal offenders who are held under Lieutenant Governor's Warrants. It explores the psychiatric-legal issues in cases of pre-trial (not fit to stand trial) and post-trial (not guilty by reason of insanity) L.G.W.'s. An attempt is made to provide a structure for such psychiatric-legal evaluations. Clinical guidelines are offered about the objectives, the assumptions and the criteria which form the basis of such evaluations. Suggestions are made for collection of relevant data which should inform psychiatric and legal judgement-making in this area. The role of the psychotropic medication in N.G.I. cases is discussed. It is recommended that whenever medically feasible, a controlled drug-free trial should be carried out in N.G.I. cases prior to their final release, in order to unambiguously establish their need for medication.

Pre-trial evaluation of court referrals

This paper examines the current Canadian laws and psychiatric practice relating to the pre-trial evaluation of court referrals in a mental hospital. The purpose of evaluation is briefly discussed. The issue of fitness to stand trial is examined in detail and psychiatric criteria of unfitness reviewed and illustrated with brief descriptions of clinical cases. It is contended that motivation for defence may be crucial in determining the fitness or unfitness of the accused. Under the present laws a finding of unfitness leads to legal and psychiatric consequences which contain elements of potential injustice to the patient. The recommendations of the Chalke Committee to modify the legal procedure and to remove some of these difficulties are underlined. The paper concludes with a description of the actual process of assessment in the hospital, the writing and submission of psychiatric reports, the fate of such reports and problems commonly encountered in the pre-trial evaluation.