Structure-Guided Discovery of Selective USP7 Inhibitors with In Vivo Activity

Inhibition of ubiquitin-specific protease 7, USP7, has been proposed as a mechanism to affect many disease processes, primarily those implicated in oncology. The bound crystal structure of a published high-throughput screening hit with low-micromolar affinity for USP7 identified three regions of the compound for structure-guided optimization. Replacing one side of the compound with different aromatic moieties gave little improvement in affinity, and the central piperidine could not be improved. However, the binding site for the other side of the compound was poorly defined in the crystal structure, which suggested a wide variety of synthetically accessible options for optimization. These were assessed by screening reaction mixtures that introduced different substituents to this other side. Subsequent optimization led to a compound with low-nanomolar affinity for USP7, which showed target engagement in tumors, was tolerated in mice, and showed efficacy in xenograft models.

Atrial-specific reduction of Kir2.1 channel pore diameter in addition to loss of inward-going rectification underlies inducible atrial fibrillation in a mouse model of short QT syndrome type 3

Introduction

Short QT Syndrome Type 3 (SQTS3) is an extremely rare arrhythmogenic disease caused by gain-of-function mutations in the KCNJ2 gene coding the inward rectifier potassium channel Kir2.1. We investigated arrhythmogenic mechanisms associated with a de-novo mutation (E299V) in Kir2.1 in an 11-year-old boy presenting an extremely abbreviated QT interval, paroxysmal atrial fibrillation, and mild left ventricular dysfunction. Amino acid E299 in the Kir2.1 sequence is necessary for polyamine binding induced inward rectification.

Purpose

Test the hypothesis that Kir2.1E299V induces reduced conductance and lack of rectification that causes electrical defects in atrial cardiomyocytes, predisposing patients to atrial arrhythmias.

Methods

We used intravenous adeno-associated virus-mediated gene transfer to generate mice expressing wild-type (WT) and the E299V mutant protein. We used ECG, intracardiac stimulation, patch-clamp, molecular biology and computational modelling to characterize the models and study arrhythmia mechanisms in the atria and ventricles.

Results

We confirmed WT or mutant Kir2.1 gene expression specifically in the mouse heart. On ECG, the corrected QT (QTc) interval of Kir2.1E299V mice was significantly shorter than Kir2.1WT mice (p<0.0001). The PR interval in Kir2.1E299V was also significantly shorter than WT mice (p<0.0001). On intracardiac stimulation, the largest proportion of arrhythmic events occurred in the atria, as 7 out of 9 Kir2.1E299V mice presented >1 second atrial flutter/fibrillation, while only 2 out of 10 Kir2.1WT mice showed this type of arrhythmia (p=0.023). On patch clamping, both atrial and ventricular cardiomyocytes expressing Kir2.1E299V had extremely abbreviated action potential durations (APD90) at all frequencies studied (p<0.0001). The current/voltage relation of ventricular Kir2.1E299V cardiomyocytes revealed an absence of inward-going rectification and increased IK1 at voltages positive to −80 mV compared to Kir2.1WT cardiomyocytes (p<0.0001). In contrast, while in the atrial Kir2.1E299V cardiomyocytes the outward IK1 was increased at voltages positive to −80 mV with loss of rectification, IK1 was significantly reduced at voltages negative to −80 mV (p<0.0001), suggesting a loss of function leading to atrial arrhythmia inducibility. A higher proportion of Kir2.2 at atrial level and atomic in-silico 3D simulations suggested that the mutation impaired polyamine block of the Kir2.1E299V-Kir2.2 channel while reducing the pore diameter.

Conclusions

This first in-vivo mouse model of cardiac-specific SQTS3 recapitulates the electrophysiological phenotype of a patient with the Kir2.1E299V mutation. The mutation results in a Kir2.1 gain-of-function mediated by and absence of rectification. The predominant arrhythmias induced in these SQTS3 mice were supraventricular likely due to the combined lack of inward rectification and atrial-specific reduced pore diameter of the Kir2.1E299V-Kir2.2 channel.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): La Caixa FoundationLa Maratό TV3 Foundation

Three dimensional modelling of mutant Kir2.1 channel PIP2 interactions help stratify arrhythmia severity in Andersen Tawil syndrome type 1

Background

Andersen-Tawil type 1 (ATS1) is associated with loss-of-function mutations in the inward rectifier potassium channel Kir2.1, which controls cardiac excitability and impulse conduction. Phosphatidylinositol-4,5-bisphosphate (PIP2) acts as an essential cofactor regulating the opening of Kir2.1 channels. Fifty percent of reported ATS1 mutations affect Kir2.1-PIP2 interactions, leading to ECG defects, ventricular arrhythmias and sudden cardiac death (SCD) by mechanisms that are poorly understood.

Purpose

To test the hypothesis that the degree of arrhythmogenic severity of ATS1 mutations disrupting PIP2-Kir2.1 binding may be predicted by the level of polarization of the mutant Kir2.1 channel pore.

Methods

We first used a statistical mean value approach to classify the 40 known arrhythmogenic ATS1 mutations impacting Kir2.1-PIP2 interaction (N=260 individuals) according to arrhythmogenic severity, ranging from SCD through ventricular bigeminy and QT prolongation. We then generated 3D in-silico atomic models of the wildtype channel and the 10 mutant channels with the most severe arrhythmic phenotype to assess the mechanism of the structural defects associated with Kir2.1-PIP2 disruption.

Results

Our cardiac lethality scoring stratifying Kir2.1 mutations according to arrhythmogenic severity was validated by three additional biostatical quantitative measures. On in-silico modelling, wildtype Kir2.1 channels without PIP2 binding had transmembrane and cytoplasmic pore radius of 1.5 and 3 Å, respectively. Kir2.1-PIP2 interactions increased transmembrane and cytoplasmic pore radius to 3 and 6 Å, respectively. All 10 Kir2.1 mutations had similar transmembrane and cytoplasmic pore radius of ∼1.0 and ∼3.0 Å, respectively. The most severe mutations yielded pore channels with highly polarized electrostatic forces. Remarkably, simulations showed a descending electrostatic pattern at the transmembrane region of PIP2 binding, where the more severe the mutation, the more positive that region was. Structural changes produced by mutations correlated with cardiac severity (R2=0.51; p<0.005) in that the most drastically altered protein structure correlated with the most severe arrhythmic phenotype.

Conclusions

Computer simulations of mutant Kir2.1 channel structure from the most arrhythmogenic to the least arrhythmogenic predict a gradual decrease in polarization of electrostatic forces along the Kir2.1 channel pore. The results reveal a novel mechanistic stratification of arrhythmogenic severity of ATS1 mutant Kir2.1 channel-PIP2 interactions and open new pathways for developing more personalized ATS1 patient therapies.

Funding Acknowledgement

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): La Caixa Banking Foundation under the project code HR18-00304Fundaciόn La Marato TV3: Ayudas a la investigaciόn en enfermedades raras 2020

Common light chain chickens produce human antibodies of high affinity and broad epitope coverage for the engineering of bispecifics

Bispecific antibodies are an important and growing segment in antibody therapeutics, particularly in the immuno-oncology space. Manufacturing of a bispecific antibody with two different heavy chains is greatly simplified if the light chains can be the same for both arms of the antibody. Here, we introduce a strain of common light chain chickens, called OmniClic®, that produces antibody repertoires largely devoid of light chain diversity. The antibody repertoire in these chickens is composed of diverse human heavy chain variable regions capable of high-affinity antigen-specific binding and broad epitope diversity when paired with the germline human kappa light chain. OmniClic birds can be used in immunization campaigns for discovery of human heavy chains to different targets. Subsequent pairing of the heavy chain with a germline human kappa light chain serves to facilitate bispecific antibody production by increasing the efficiency of correct pairing.

Abbreviations: AID: activation-induced cytidine deaminase; bsAb: bispecific antibody; CDR: complementarity-determining region; CL: light chain constant region; CmLC: common light chain; D: diversity region; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell sorting; Fc: fragment crystallizable; FcRn: neonatal Fc receptor; FR: framework region; GEM: gel-encapsulated microenvironment; Ig: immunoglobulin; IMGT: the international ImMunoGeneTics information system®; J: joining region; KO: knockout; mAb: monoclonal antibody; NGS: next-generation sequencing; PBS: phosphate-buffered saline; PCR: polymerase chain reaction; PGC: primordial germ cell; PGRN: progranulin; TCR: T cell receptor; V: variable region; VK: kappa light chain variable region; VL: light chain variable region; VH: heavy chain variable region

Abstract B163: Identification and preclinical characterisation of VER-250840, a potent, selective Chk1 inhibitor with in vivo oral single-agent antitumor activity

On sustaining damage to their DNA, cells employ a sophisticated mechanism of detection and repair, termed the DNA damage response (DDR). As a critical component of the DDR and G2/M checkpoint, Chk1 kinase represents an attractive target for cancer therapy. We have utilized a structure-based drug design approach to identify and develop VER-250840, a novel, orally active inhibitor of the checkpoint kinase, Chk1. VER-250840 exhibited sub-nM potency against Chk1 kinase with exquisite selectivity over an extensive and diverse panel of kinases. In vitro, VER-250840 inhibited Chk1 autophosphorylation with an IC50 of 1.0 nM and increased the number of S-phase tumor cells staining positive for pan-nuclear γH2AX with an EC50 of 7 - 27 nM. Accumulated genomic DNA damage by Chk1 inhibition led to irreversible cell cycle arrest, inhibition of tumor cell proliferation, increased replication stress, and cell death in both 2D culture and multicellular tumor spheroids. In an in vivo A2058 tumor xenograft PD study, VER-250840 demonstrated rapid and sustained inhibition of Chk1 auto-phosphorylation within 30 minutes of oral administration. Doses of 10 mg/kg and higher PO resulted in greater than 90% inhibition of tumor pChk1 (S296) over 24 hours. In SKOV3 in vivo models, VER-250840 inhibited Chk1 auto-phosphorylation, modulated other biomarkers of replication stress and DNA damage, and exhibited moderate antitumor activity with minimal toxicity when administered orally on a 21-day once-daily schedule. Work is ongoing to further optimize in vivo efficacy. In conclusion, VER-250840 demonstrates potent and selective activity as a monotherapy both in vitro and in vivo. From these findings, further evaluation and optimization of this novel kinase inhibitor is justly merited.

Citation Format: Joanne Wayne, Stephen Stokes, Nicolas Foloppe, Helen Browne, Teresa Brooks, Karen Benwell, Lisa Baker, Zoe Daniels, Andrea Fiumana, Christopher Graham, Alba Macias, Daniel Maddox, Sean McKenna, Christopher Northfield, Stuart Ray, Heather Simmonite, Emma Stefaniak, Paul Webb, Mike Wood, Andrew Massey. Identification and preclinical characterisation of VER-250840, a potent, selective Chk1 inhibitor with in vivo oral single-agent antitumor activity [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B163.

VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and induces context-dependent cytostasis in cancer cells

Pyruvate dehydrogenase kinase (PDK) is a pivotal enzyme in cellular energy metabolism that has previously been implicated in cancer through both RNAi based studies and clinical correlations with poor prognosis in several cancer types.

Here, we report the discovery of a novel and selective ATP competitive pan-isoform inhibitor of PDK, VER-246608. Consistent with a PDK mediated MOA, VER-246608 increased pyruvate dehydrogenase complex (PDC) activity, oxygen consumption and attenuated glycolytic activity. However, these effects were only observed under D-glucose-depleted conditions and required almost complete ablation of PDC E1α subunit phosphorylation. VER-246608 was weakly anti-proliferative to cancer cells in standard culture media; however, depletion of either serum or combined D-glucose/L-glutamine resulted in enhanced cellular potency. Furthermore, this condition-selective cytostatic effect correlated with reduced intracellular pyruvate levels and an attenuated compensatory response involving deamination of L-alanine. In addition, VER-246608 was found to potentiate the activity of doxorubicin. In contrast, the lipoamide site inhibitor, Nov3r, demonstrated sub-maximal inhibition of PDK activity and no evidence of cellular activity.

These studies suggest that PDK inhibition may be effective under the nutrient-depleted conditions found in the tumour microenvironment and that combination treatments should be explored to reveal the full potential of this therapeutic strategy.

Abstract B155: VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and demonstrates context-dependent cytotoxicity to cancer cells

Pyruvate dehydrogenase kinase (PDK) regulates the activity of the pyruvate dehydrogenase complex (PDC) through phosphorylation of three serine residues on the E1α subunit, resulting in decreased activity. The expression of all four mammalian isoforms of PDK have been shown to be up-regulated either under tumour relevant conditions (PDK-1 & PDK-3 by hypoxia) or by the loss of function of common tumour suppressor genes (PDK-2 by p53; PDK-4 by pRB). Furthermore, PDK-1 expression has been clinically correlated with poor prognosis in Gastric, HNSCC and Colon cancer. Previous studies employing RNAi have provided evidence for a survival role for PDK-1 as well as its importance in maintaining the glycolytic phenotype of cancer cells. DCA, a weak inhibitor of PDK, has also been used to study the role of PDK in cancer; however, interpretation of these studies has been complicated by conflicting data and the lack of specificity of this agent for PDK. Here we report the discovery of a novel, potent and selective pan-isoform inhibitor of PDK, VER-246608. Consistent with a PDK mediated MOA, treatment of PC-3 cells with VER-246608 resulted in increased PDC activity and oxygen consumption as well as reduced lactate production and glucose consumption. Interestingly, modulation of glycolytic activity required compound concentrations which achieved > 90 % reduction in E1α phosphorylation and this was only observed under glucose depleted conditions. Under normal culture conditions, VER-246608 showed little cytotoxicity to cancer cells. We hypothesised that the supraphysiological glucose concentrations present in cell culture media may limit the effect of PDK inhibition due to elevated intracellular pyruvate levels. We therefore performed cytotoxicity studies under conditions of limited nutrient availability. We found that combined depletion of glucose and glutamine or serum alone resulted in enhanced cytotoxicity vs normal media; however, hypoxic conditions had no effect. Furthermore, this differential cytotoxicity correlated with reduced pyruvate levels in the compound treated cells cultured in the above ‘austere’ conditions. VER-246608 also inhibited the growth of tumour spheroids with a potency that was comparable to cells grown in 2D culture. In addition, combination treatment studies revealed that VER-246608 potentiated anti-cancer agents which are known to influence mitochondrial function. In contrast, the lipoamide binding site inhibitor, Nov3r, showed no evidence of cytotoxicity under any of the above conditions and was ineffective in altering glycolytic activity. These studies suggest that PDK inhibition may be effective under the nutrient depleted conditions found in the tumour microenvironment and that combination treatments should be explored to reveal the full potential of this therapeutic strategy.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B155.

Citation Format: Jonathan Moore, Anna Staniszewska, Terence Shaw, Jalanie D'Alessandro, Ben Davis, Alan Surgenor, Lisa Baker, Natalia Massanova, James Murray, Alba Macias, Paul Brough, Mike Wood, Patrick C. Mahon. VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts Warburg metabolism and demonstrates context-dependent cytotoxicity to cancer cells. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B155.

Cognitive declines following bilateral subthalamic nucleus deep brain stimulation for the treatment of Parkinson's disease

BACKGROUND

We investigated the cognitive and psychiatric outcome 6 months after bilateral subthalamic nucleus deep brain stimulation (DBS) for the treatment of Parkinson's disease (PD) using a disease control group.

METHODS

23 patients who underwent DBS were compared with 28 medically treated patients with PD at baseline and at 6 months for neuropsychological measures. In addition to the group outcomes, we report reliable change indices (RCI) and a dementia caseness analysis.

RESULTS

Patients who underwent DBS demonstrated a significant decline in verbal memory compared with the control group (p<0.003), and trends for decline on oral information processing, including verbal fluency, timed transcription and word naming. Patients who underwent DBS demonstrated declines in attention, set shifting and semantic fluency but these changes were similar to the rate of decline in the PD group. RCI indicated that patients who underwent DBS demonstrated clinically significant declines in verbal fluency (p<0.01) and inhibition of a dominant response (p<0.003), with trends for declines in set shifting (p<0.02) and verbal long term recall (p<0.08), indicative of frontostriatal dysfunction. Patients who underwent DBS did not demonstrate significant changes in depression, anxiety or psychological distress scores. The caseness analysis revealed that one of the patients who underwent DBS (4%) converted to dementia over 6 months compared with none of the PD controls.

CONCLUSIONS

Our findings demonstrated that patients who underwent DBS experienced declines in verbal recall and trends for declines in oral information processing 6 months following surgery, even when good motor outcome was achieved. Potential candidates should be counselled about the risk of mild frontostriatal cognitive declines following DBS to weigh the risks and benefits of surgery.

Short and long-term motor and cognitive outcome of staged bilateral pallidotomy: a retrospective analysis

BACKGROUND

We investigated retrospectively the short and long-term motor and cognitive functioning of staged bilateral pallidotomy using motor testing and a comprehensive neuropsychological battery before and after each procedure.

METHODS

Fifteen patients with idiopathic Parkinson's disease were assessed at baseline and at least 3 months after each of their two staged surgeries. Motor and neuropsychological results were compared to 15 non-surgical Parkinson's disease patients matched for disease stage and mental status. In addition, nine bilateral pallidotomy patients were evaluated for long-term cognitive changes (>2 years).

FINDINGS

Bilateral pallidotomy patients demonstrated significant improvements in motor functioning in the "on" and "off" states and with dyskinesias after the first surgery, with an additional improvement reported for dyskinesias after the second procedure. On long-term follow-up, dyskinesia improvements were maintained. Bilateral pallidotomy patients did not show significant cognitive declines following both procedures on the short-term follow-up and when compared to the Parkinson's disease group. However, significant cognitive declines were found on the long-term follow-up evaluation.

CONCLUSIONS

Parkinson's disease patients received significant short- and long-term motor benefits, particularly reduced dyskinesias, following staged bilateral pallidotomy without significant short-term cognitive consequences. Two years following the second procedure, bilateral pallidotomy patients tended to show an increase in both motor and non-motor symptoms of Parkinson's disease, particularly cognitive decline.

Identification of novel extracellular signal-regulated kinase docking domain inhibitors

The extracellular signal regulated kinase (ERK1 and ERK2) signal transduction pathways play a critical role in cell proliferation. Hyperactivation of the ERK proteins either through increased expression of membrane-bound growth factor receptors or genetic mutations of upstream proteins is thought to be involved in the pathogenesis of many human cancers. Thus, targeted inhibition of ERK signaling is viewed as a potential approach to prevent cancer cell proliferation. Currently, no specific inhibitors of the ERK proteins exist. Moreover, most kinase inhibitors lack specificity because they target the ATP binding region, which is well conserved among the protein kinase families. Taking advantage of recently identified ERK docking domains, which are reported to facilitate substrate protein interactions, we have used computer-aided drug design (CADD) to identify novel small molecular weight ERK inhibitors. Following a CADD screen of over 800 000 molecules, 80 potential compounds were selected and tested for activity in biological assays. Several compounds inhibited ERK-specific phosphorylation of ribosomal S6 kinase-1 (Rsk-1) or the ternary complex factor Elk-1 (TCF/Elk-1), both of which are involved in promoting cell proliferation. Active compounds showed a dose-dependent reduction in the proliferation of several cancer cell lines as measured by colony survival assays. Direct binding between the active compounds and ERK2 was indicated by fluorescence quenching. These active compounds may serve as lead candidates for development of novel specific inhibitors of ERK-substrate interactions involved in cell proliferation.