V-SYNTHES-guided discovery of BET bromodomain inhibitors : a novel antifungal strategy against Candida auris
New antifungal strategies are urgently needed to combat Candida auris, an emerging multidrug-resistant fungal "superbug" responsible for severe hospital outbreaks and high-mortality infections. Our previous proof-of-concept studies in Candida albicans and Candida glabrata established that fungal BET bromodomains – chromatin-binding modules that recognize acetylated histones – represent promising new antifungal targets. We have developed an advanced set of molecular and cellular tools to accelerate antifungal BET inhibitor discovery, including FRET-based assays for compound screening, humanized Candida strains for on-target validation, and NanoBiT assays to monitor BET bromodomain inhibition directly in fungal cells.
This PhD project represents the translational next phase of our research program. It will exploit the AI-guided V-SYNTHES drug discovery approach – a cutting-edge virtual screening and design framework – to develop highly potent BET inhibitors targeting C. auris. Inhibitors will be profiled in biophysical, biochemical and cellular assays, structurally characterized in complex with their bromodomain targets, and validated for on-target activity in C. auris and antifungal efficacy in animal infection models. They will also be used to explore the emergence of resistance to BET inhibition. This project combines an original antifungal strategy with an innovative methodological approach, offering a unique framework for training in interdisciplinary and translational research.
Development of a Modular Enzymatic Platform for the In Silico Design and Synthesis of Novel Therapeutic Peptides via Protein Splicing
The rise of antimicrobial resistance (AMR) has developed into a slow-moving epidemic, fueled by the overuse and misuse of antibiotics, coupled with a stagnation in the development of new antimicrobial agents over the past four decades. Addressing this crisis requires not only more judicious use of existing antibiotics but also the development of innovative drugs capable of overcoming resistant pathogens. In this context, the abundant genomic data generated in the omics era has facilitated the resurgence of natural products as a vital source of novel compounds. Among these, natural peptides—with their unique and diverse chemical properties—have garnered particular interest as potential antibiotics, anticancer agents, and inhibitors targeting specific pathological processes.
The aim of this PhD project is to develop a novel, modular enzymatic tool that enables the in silico design and synthesis of peptides with unprecedented chemical diversity. Central to this approach is the exploitation of a unique chemical reaction: protein splicing. This innovative reaction allows precise removal or editing of specific peptidic sequences, thereby providing a powerful platform to generate hybrid peptides with tailored functionalities, including potential therapeutic agents.
This project will integrate structural and functional studies, computational peptide design and enzyme engineering, aiming to expand the chemical and functional diversity of peptide-based molecules. The successful candidate will work in a state-of-the-art research setting, equipped with cutting-edge facilities and collaborative opportunities, fostering innovative approaches and impactful contributions to the field.
Real-space fitting of flexible molecular structures in high-speed AFM topographic movies
Structural biology seeks to understand the function of macromolecules by determining the precise position of their atoms. Its traditional methods (X-ray crystallography, NMR, electron microscopy), although effective, offer a static view of macromolecules, limiting the study of their dynamics. A new paradigm is emerging: integrative structural biology, combining several techniques to capture, among other things, molecular dynamics. However, despite improvements in femtosecond serial crystallography, molecular dynamics simulations, and cryo-electron tomography, current methods struggle to reach the functional time scale (milliseconds to seconds).
The advent of new scanning probe microscopy, and in particular the recent development of high-speed atomic force microscopy (HS-AFM), allows molecular movements to be observed on the millisecond scale, but lacks the atomic resolution to revolutionize structural biology. The objective of the proposed topic is to further exploit the use of HS-AFM by modeling detailed atomic structures at the heart of the images obtained. The tasks will be both biophysical and computational, involving the improvement of the existing AFM-Assembly tool, which allows direct spatial adjustment of the atomic coordinates of the target molecule under AFM topography. The aim is to apply this protocol to a new type of big data, namely topographical movies obtained by high-speed AFM.
The thesis will be conducted at the Institute of Structural Biology in Grenoble, within the Methods and Electron Microscopy (MEM) group of the Grenoble Interdisciplinary Research Institute (IRIG). It will be carried out in collaboration with the DyNaMo laboratory in Marseille, which specializes in high-speed AFM data acquisition, as part of a joint ANR funding application.
The scientific interest of the project is major for modern integrative structural biology. The great scientific challenge of the coming years in structural biology is the study and analysis of molecular dynamics, in order to move beyond the current paradigm (instantaneous photography) and participate in the emergence of a new paradigm (real-time movie).
Dynamic interplay of Rad51 nucleoprotein filament-associated proteins - Involvement in the regulation of homologous recombination
Homologous recombination (HR) is an important mechanism for the repair of ionizing radiation- induced DNA double-strand breaks. A key step in HR is the formation of Rad51 nucleoprotein filaments on the single-stranded DNA that is generated from these breaks. We were the first to show, using yeast as a model, that a tight control of the formation of these filaments is essential for HR not to induce chromosomal rearrangements by itself (eLife 2018, Cells 2021, Nat. Commun. 2025). In humans, the functional homologs of the yeast control proteins are tumor suppressors. Thus, the control of HR seems to be as important as the mechanism of HR itself. Our project involves the use of new molecular tools that allow a breakthrough in the study of these controls. We will use a functional fluorescent version of the Rad51 protein, developed for the first time by our collaborators A. Taddei (Institut Curie), R. Guérois and F. Ochsenbein (I2BC, Joliot, CEA). This major advance will allow us to observe the influence of regulatory proteins on DNA repair by microscopy in living cells. We have also developed highly accurate structural models of control protein complexes associated with Rad51 filaments. We will adopt a multidisciplinary approach based on genetics, molecular biology, biochemistry, and protein structure to understand the function of the regulators of Rad51 filament formation. The description of the organization of these proteins with Rad51 filaments will allow us to develop new therapeutic approaches.