Biology subjects

Biondi, R. M.

Publications and source records attributed to Biondi, R. M..

3 recordsLinked to original sources

bioRxiv2025

Sodium Aurothiomalate Induces Ferroptosis by Targeting GPX4 via Gold-Dependent Thiomalate Covalent Modification

Ferroptosis, an iron-dependent form of oxidative cell death, is predominantly regulated by glutathione peroxidase 4 (GPX4), making it a promising target for cancer therapy. However, the majority of GPX4 inhibitors, most of which contain a chloroacetamide moiety such as RSL3, are limited by poor pharmacokinetic properties and off-target effects, hindering their preclinical translation. Utilizing a range of interdisciplinary methodologies, we show that sodium aurothiomalate (ATM), a drug approved by many agencies, induces ferroptosis by covalently targeting GPX4 via formation of a selenenylsulfide bond. In preclinical models of neuroblastoma and acute myeloid leukemia (AML), ATM combined with ferric ammonium citrate (FAC) yields a synergistic effect, resulting in a significant reduction in tumor growth. Mechanistically, ATM disrupts GPX4 activity by covalently binding thiomalate to the active site selenocysteine, while modification of specific cysteine residues leads to destabilization of the protein and impaired binding to phospholipids. We propose that these covalent modifications are achieved through a unique reaction mechanism, in which the gold component of ATM acts as a thiol-masking carrier and is only transiently present, being subsequently displaced and allowing the reaction of the thiomalate moiety with the target selenocysteine or cysteine. Our data lay the foundation for development of novel, drug-like thiol-based GPX4 inhibitors.

biochemistry↗

bioRxiv2021

A TPR scaffold couples signal detection to OdhI phosphorylation in metabolic control by the protein kinase PknG

Signal transduction is essential for bacteria to adapt to changing environmental conditions. Among many forms of post-translational modifications, reversible protein phosphorylation has evolved as a ubiquitous molecular mechanism of protein regulation in response to specific stimuli. The Ser/Thr protein kinase PknG modulates the fate of intracellular glutamate by controlling the phosphorylation status of the 2-oxoglutarate dehydrogenase regulator OdhI, a function that is conserved among diverse actinobacteria. PknG has a modular organization characterized by the presence of regulatory domains surrounding the catalytic domain. Here we present an investigation through in vivo experiments as well as biochemical and structural methods of the molecular bases of the regulation of PknG from C. glutamicum (CgPknG), in the light of previous knowledge available for the kinase from M. tuberculosis (MtbPknG). We found that OdhI phosphorylation by CgPknG is regulated by a conserved mechanism that depends on a C-terminal domain composed of tetratricopeptide repeats (TPR) essential for metabolic homeostasis. Furthermore, we identified a conserved structural motif that physically connects the TPR domain and a flexible N-terminal extension of the kinase that is involved in docking interactions with OdhI. Based on our results and previous reports, we propose a model in which the TPR domain of PknG couples signal detection to the specific phosphorylation of OdhI. Overall, the available data indicate that conserved PknG domains in distant actinobacteria retain their roles in kinase regulation in response to nutrient availability. IMPORTANCEBacteria control the metabolic processes by which they obtain nutrients and energy in order to adapt to the environment. In this way, the metabolic characteristics of a microorganism determine its ecological role and its usefulness in industrial processes. Here, we use genetic, biochemical, and structural approaches to study a key component in a system that regulates glutamate production in C. glutamicum, a species that is used for the industrial production of amino acids. We elucidated molecular mechanisms involved in metabolic control in C. glutamicum, which are conserved in related pathogenic bacteria. The findings have broader significance for diverse actinobacteria, including microorganisms that cause disease as well as environmental species used to produce billions of dollars of amino acids and antibiotics every year.

biochemistry↗

bioRxiv2018

Proteome-scale detection of drug-target interactions using correlations in transcriptomic perturbations

The development of an expanded chemical space for screening is an essential step in the challenge of identifying chemical probes for new, genomic-era protein targets. However, the difficulty of identifying targets for novel compounds leads to the prioritization of synthesis linked to known active scaffolds that bind familiar protein families, slowing the exploration of available chemical space. To change this paradigm, we validated a new pipeline capable of identifying compound-protein interactions even for compounds with no similarity to known drugs. Based on differential mRNA profiles from drug treatments and gene knockdowns across multiple cell types, we show that drugs cause gene regulatory network effects that correlate with those produced by silencing their target protein-coding gene. Applying supervised machine learning to exploit compound-knockdown signature correlations and enriching our predictions using an orthogonal structure-based screen, we achieved top-10/top-100 target prediction accuracies of 26%/41%, respectively, on a validation set 152 FDA-approved drugs and 3104 potential targets. We further predicted targets for 1680 compounds and validated a total of seven novel interactions with four difficult targets, including non-covalent modulators of HRAS and KRAS. We found that drug-target interactions manifest as gene expression correlations between drug treatment and both target gene knockdown and up/down-stream knockdowns. These correlations provide biologically relevant insight on the cell-level impact of disrupting protein interactions, highlighting the complex genetic phenotypes of drug treatments. Our pipeline can accelerate the identification and development of novel chemistries with potential to become drugs by screening for compound-target interactions in the full human interactome.

genomics↗