Structural snapshots of a substrate within the active site of a mitogen-activated protein kinase
Mitogen-activated protein kinases (MAPKs) are key signaling enzymes that regulate cellular stress responses through the phosphorylation of specific protein substrates. Dysregulation of MAPK signaling contributes to numerous diseases, including cancer and neurodegenerative disorders. Although MAPK activation and catalytic mechanisms are well characterized, the structural basis of substrate specificity remains unknown. This project aims to address this gap by capturing atomic-level structural snapshots of substrates bound within the active site of the c-Jun N-terminal kinase 1 (JNK1). To achieve this, we will employ X-ray crystallography together with innovative nuclear magnetic resonance (NMR) methods that integrate selective methyl isotope labeling and photoactivatable catalysis. By elucidating the structural details of how substrates are recognized by the active site of JNK1, our work will open new avenues for the development of substrate-competitive inhibitors of MAPKs with enhanced selectivity and therapeutic potential.
Adaptation and degradation of PFAS by the bacterium Pseudomonas putida
Per- and polyfluoroalkyl substances (PFASs) are a class of very diverse chemicals found in products of daily use, that are highly persistent and encountered everywhere in the environment. They accumulate/biomagnify within the natural food chain and show a relatively high toxicity including the alternative products developed after the ban of the legacy compounds. Therefore, the world is facing a situation of great concern all the more as the retreatment of contaminated soils, sediments and water is difficult and costly. One of the main challenges is because various PFASs have quite different physicochemical properties but are often encountered in mixture making it difficult to find a technology efficient to remove all of them. We propose to pave the way towards another approach for PFASs elimination, bioremediation that is known to be a good alternative to chemical or physical methods for removing toxics (self-sustainability, cheaper, working in milder conditions, and often with dissolved and sorbed contaminants). A few bacteria have been described to be able to partially modify/degrade some PFASs. However, except the aspect of PFAS transformation, no data are available concerning their adaptation to PFAS exposure. A few projects are focusing on finding enzymes implicated in the degradation per se but if we want to use bacterial cultures and not enzymes, many other parameters need to be taken into account to set up a performant strain and hence a performant process. Therefore, we propose to analyze in depth the response to several PFASs of the PFAS degrading strain Pseudomonas putida ATCC 17514 in term of degradation, adaptation to a potential toxicity and metabolism adjustment. The analyses will mainly rely on a proteomic approach that is a very powerful technique to analyze global responses without a priori, and has never been done to characterize PFASs toxicity or fluorinated compounds metabolism in bacteria. The ultimate goal after this bootstrap project will be to engineer or select a robust and efficient strain capable of biodegrading PFASs.
III-V semiconductor nanoplatelets
Colloidal semiconductor nanoplatelets (NPLs) are a class of two-dimensional nanostructures that have electronic and optical properties distinct from those of spherical quantum dots (QDs). They exhibit strong quantum confinement in a single dimension, their thickness, which can be controlled on the monolayer level using solution chemistry. As a result, NPLs emit light with an extremely narrow spectral width and at the same time, they have a very high absorption coefficients. These properties make them ideal candidates for various applications (e.g., light-emitting diodes for low-power-consumption displays, photocatalysis, single-photon emitters).
At present, only the synthesis of metal chalcogenide NPLs has been mastered. These materials either contain toxic elements (CdSe, HgTe, etc.) or have a large bandgap (ZnS, ZnSe). For these reasons, the development of synthesis methods for III-V semiconductor NPLs, such as InP, InAs and InSb is currently a major challenge. In this thesis, we will develop new synthetic approaches for the growth of InP NPLs, exploring different avenues and using in situ characterizations as well as machine learning assisted design of experiments. Numerical simulations will be used to determine the reactivity of precursors and to model the mechanisms inducing anisotropic growth.
Active matter: self-organization of mitotic spindles
The mitotic spindle is an essential cytoskeletal structure that enables chromosome separation during cell division. This project seeks to identify the physical principles that control spindle assembly by using a simplified biomimetic system composed solely of microtubules and molecular motors. We will use motors of opposite polarities combined with dynamic microtubules to understand how these components organize through active phase separation. Indeed, preliminary experiments have demonstrated that such reconstituted systems can spontaneously form bipolar structures resembling mitotic spindles. We now propose to encapsulate these molecular components in compartments of controlled geometry to reconstruct a minimal bipolar structure capable of elongating, retracting, and separating its organizing poles. This multidisciplinary approach will combine biochemical and physicochemical techniques, advanced microscopy, and quantitative analysis of the spatial and temporal evolution of the system. The experimental work will be closely coupled with theoretical modeling in collaboration with Prof. Jean-François Joanny (Collège de France) to develop a physical model of active phase separation that will provide better understanding of self-organization mechanisms at the subcellular scale in living organisms.
Endothelial-fibroblast interactions in diabetic foot ulcer: deciphering the intercellular communication responsible for the chronic wound persistence
Diabetic foot ulcer (DFU), a severe complication of diabetes affecting approximately 18.6 million people worldwide each year, is associated with high rates of amputation and mortality. Like other chronic wounds, DFUs exhibit impaired healing due to a dysregulated cascade of cellular signalling and behavioural events that normally ensure rapid closure of the skin barrier. Among the key cellular players, fibroblasts and endothelial cells are central to the proliferative and remodelling phases of wound repair – processes that are notably dysfunctional in chronic wounds. Although endothelial-fibroblast crosstalk is recognized as an essential driver of normal skin healing, the specific mechanisms governing their interaction in DFU is poorly understood.
The main objective of this PhD project is to decipher the intercellular communication between endothelial cells and fibroblasts that underlies the chronicity of DFU. Particular attention will be devoted to extracellular vesicle-associated microRNAs (miRNAs), which are pivotal regulators of intercellular communication through modulation of gene expression in recipient cells. By characterizing the repertoire of pro- and anti-healing miRNAs exchanged between endothelial cells and fibroblasts, this project seeks to uncover novel molecular targets and therapeutic strategies to promote wound repair in diabetic foot ulcers.
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.
The combined effects of hypoxia and matrix stiffness on the pathophysiology of pulmonary fibrosis.
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal lung disease characterized by excessive extracellular matrix (ECM) deposition, increased tissue stiffness, and localized hypoxia. These alterations disrupt cell–cell interactions within the alveolo-capillary barrier and drive fibrotic progression. This project aims to investigate, under controlled in vitro conditions, the combined impact of mechanical stiffness and hypoxic stress on the fate and phenotype of pulmonary cell types and their intercellular communication. To achieve this, biomimetic polyacrylamide hydrogels with tunable stiffness and specific ECM protein coatings will be developed to support the co-culture of alveolar epithelial cells, endothelial cells, fibroblasts, and macrophages. Cellular responses will be assessed through proteomics, imaging, and secretome profiling. The goal is to identify key mechano- and chemo-dependent pro-fibrotic factors, providing new insights into IPF pathogenesis and opening avenues for targeted therapeutic strategies and lung tissue regeneration.
Studying the structural dynamics of vitamin B12 -dependent photoreceptors in view of biotechnological applications
This integrated structural biology project aims at gaining a mechanistic understanding of the recently discovered family of vitamin B12 -dependent photoreceptors. In particular, we aim at visualising protein conformational changes upon photoactivation from the photochemical timescales (femtoseconds) to the photobiological timescales (milliseconds -seconds). To do so, we will use time-resolved X-ray crystallography and X-ray solution scattering at X-ray free electron lasers (XFEL) and at synchrotrons. By establishing the modus operandi of these newly discovered B12 photoreceptors we will open a window to their rational modification for biotechnological exploitation as optogenetic components.
PtSeipin : linking lipid droplets biogenesis and degradation in the diatom Phaeodactylum tricornutum
Microalgae encompass a wide diversity of organisms and have attracted increasing interest due to their ability to produce biomolecules of biotechnological and industrial relevance. In particular, they can accumulate oil within lipid droplets (LDs) in response to abiotic stresses such as nitrogen deprivation. This oil accumulation holds great potential for biofuel production.We recently demonstrated that knockout of the gene encoding Seipin, a protein involved in LD biogenesis, leads to a strong oil accumulation in the diatom Phaeodactylum tricornutum. Moreover, this accumulation appears to result from an absence of LD degradation in the Seipin-deficient mutants. These findings suggest that, in this diatom, LDs are programmed to undergo degradation soon after their formation, thus inhibiting LD degradation could prove a promising strategy to increase their oil content.This project aims to elucidate the mechanisms underlying LD degradation and, more specifically, the connections between their biogenesis and degradation. Three main research axes will be pursued:
1. Identify PtSeipin interaction partners involved in LD degradation, using both candidate-based and unbiased approaches.
2. Characterize the LD degradation pathways disrupted in PtSeipin knockout mutants by combining electron microscopy with transcriptomic and proteomic analyses.
3. Investigate how microalgae utilize oil during the recovery phase after stress, through fluxomic approaches.
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.