Biology subjects

Barakat, K.

Publications and source records attributed to Barakat, K..

4 recordsLinked to original sources

bioRxiv2025

Epigenetic Control of TERRA by FTSJ3 is Critical for Telomerase-Driven Cancers

Telomerase reverse transcriptase (hTERT) overexpression, a hallmark of most cancers, drives tumorigenesis by enabling limitless replicative potential. Direct targeting of hTERT is challenging, necessitating alternative strategies. Through genome-wide synthetic dosage lethality (SDL) screening in cancer models, including patient-derived organoids, we identify FTSJ3, an RNA 2-O-methyltransferase, as a critical vulnerability in hTERT-overexpressing cells. FTSJ3 methylates telomeric repeat-containing RNA (TERRA), a modification essential for recruiting SUV39H1 to telomeric ends to mediate H3K9 trimethylation and establish stable heterochromatin. Loss of FTSJ3 disrupts this cascade, impairing H3K9 trimethylation, HP1-alpha recruitment, and telomeric heterochromatin maintenance. Notably, this reveals an unexpected dependency on TERRA methylation for telomeric heterochromatin stability in hTERT-driven cancers. Non-malignant cells, lacking telomerase activity and de novo telomere repeat synthesis, are unaffected by FTSJ3 suppression. Our findings establish the FTSJ3/TERRA/SUV39H1 axis as a critical mechanism supporting telomeric heterochromatin stability in hTERT-driven cancers. This telomere-directed epigenetic strategy provides a robust framework for translational therapeutic innovation.

cancer biology↗

bioRxiv2024

The Sodium/Glucose Cotransporter 2 Inhibitor Empagliflozin Inhibits Long QT 3 Late Sodium Currents in a Mutation Specific Manner

BackgroundSodium/glucose cotransporter 2 inhibitors (SGLT2is) such as empagliflozin have demonstrated substantial cardioprotective effects in patients with or without diabetes. The SGLT2is have been shown to selectively inhibit the late component of cardiac sodium current (late INa). Induction of late INa is also the primary mechanism involved in the pathophysiology of congenital long QT syndrome type 3 (LQT3) gain-of-function mutations in the SCN5A gene that encodes the major cardiac sodium channel isoform Nav1.5. Therefore, we investigated the effect of empagliflozin on late INa in thirteen known LQT3 mutations located in distinct regions of the channel structure. MethodsThe whole-cell patch-clamp technique was used to investigate the effect of empagliflozin (10 {micro}M) on late INa in recombinantly expressed Nav1.5 channels containing different LQT3 mutations. Molecular modeling of human Nav1.5 and simulations in a mathematical model of human ventricular myocytes were used to extrapolate our experimental results to excitation contraction coupling. ResultsEmpagliflozin selectively inhibited late INa in LQT3 mutations residing in the inactivation gate region of Nav1.5, with no effect on either peak current or channel kinetics. In contrast, empagliflozin caused inhibition of both peak and late INa in mutations in the S4 voltage-sensing regions as well as changes in activation and inactivation kinetics and a slowing of recovery from inactivation. Empagliflozin had no effect on late/peak INa or channel kinetics in channels containing LQT3 mutations located in the putative empagliflozin binding region. Simulation of our experimental findings in a mathematical model of human ventricular myocytes predicts that empagliflozin may have a desirable therapeutic effect in LQT3 mutations located in the inactivation gate region. ConclusionsOur results show that empagliflozin selectively inhibits late INa, without affecting gating kinetics, in LQT3 mutations residing in the inactivation gate region. Patients with mutations in voltage-sensing regions are less suitable candidates as empagliflozin may prevent action potential firing. The SGLT2is may therefore be a promising novel precision medicine approach for patients with certain LQT3 mutations.

pharmacology and toxicology↗

bioRxiv2023

Benchmarking of Small Molecule Feature Representations for hERG, Nav1.5, and Cav1.2 Cardiotoxicity Prediction

In the field of drug discovery, there is a substantial challenge in seeking out chemical structures that possess desirable pharmacological, toxicological, and pharmacokinetic properties. Complications arise when drugs interfere with the functioning of cardiac ion channels, leading to serious cardiovascular consequences. The discontinuation and removal of numerous approved drugs from the market or at late development stages in the pipeline due to such inhibitory effects further highlight the urgency of addressing this issue. Consequently, the early prediction of potential blockers targeting cardiac ion channels during the drug discovery process is of paramount importance. This study introduces a deep learning framework that computationally determines the cardiotoxicity associated with the voltagegated potassium channel (hERG), the voltage-gated calcium channel (Cav1.2), and the voltage-gated sodium channel (Nav1.5) for drug candidates. The predictive capabilities of three feature representations--molecular fingerprints, descriptors, and graph-based numerical representations-- are rigorously benchmarked. Additionally, a novel training and evaluation dataset framework is presented, enabling predictive model training of drug off-target cardiotoxicity using a comprehensive and large curated dataset covering these three cardiac ion channels. To facilitate these predictions, a robust and comprehensive small molecule cardiotoxicity prediction tool named CToxPred has been developed. It is made available as open source under the permissive MIT license at https://github.com/issararab/CToxPred.

pharmacology and toxicology↗

bioRxiv2020

A Deep Dive into the SARS-Cov-2 Polymerase Assembly: Identifying Novel Allosteric Sites and Analyzing the Hydrogen Bond Networks and Correlated Dynamics

Replication of the SARS-CoV-2 genome is a fundamental step in the virus life cycle and inhibiting the SARS-CoV2 replicase machinery has been proven recently as a promising approach in combating the virus. Despite this recent success, there are still several aspects related to the structure, function and dynamics of the CoV-2 polymerase that still need to be addressed. This includes understanding the dynamicity of the various polymerase subdomains, analyzing the hydrogen bond networks at the active site and at the template entry in the presence of water, studying the binding modes of the nucleotides at the active site, highlighting positions for acceptable nucleotides substitutions that can be tolerated at different positions within the nascent RNA strand, identifying possible allosteric sites within the polymerase structure and studying their correlated dynamics relative to the catalytic site. Here, we combined various cutting-edge modelling tools with the recently resolved SARS-CoV-2 cryo-EM polymerase structures to fill this gap in knowledge. Our findings provide a detailed analysis of the hydrogen bond networks at various parts of the polymerase structure and suggest possible nucleotides substitutions that can be tolerated by the polymerase complex. We also report here three "druggable" allosteric sites within the nsp12 RdRp that can be targeted by small molecule inhibitors. Our correlated motion analysis shows that the dynamics within one of the newly identified sites are linked to the active site, indicating that targeting this site can significantly impact the catalytic activity of the SARS-CoV-2 polymerase.

biophysics↗