Thèse Conception In Silico d'Inhibiteurs Peptidomimétiques des Nox H/F - Doctorat.Gouv.Fr

Établissement : Université Paris Cité École doctorale : Chimie Physique & Chimie Analytique de Paris-Centre Laboratoire de recherche : Laboratoire de Biochimie Théorique Direction de la thèse : Sophie SACQUIN-MORA ORCID 0000000227814333 Début de la thèse : 2026-10-01 Date limite de candidature : 2026-06-22T23:59:59 Ce projet de thèse vise à développer de nouveaux inhibiteurs peptidiques des NADPH oxydases (NOX1, NOX2 et NOX4), qui sont les principales sources d'espèces réactives de l'oxygène (ROS) cellulaires, et sont impliquées dans des pathologies telles que les syndromes inflammatoires, les maladies neurodégénératives et les maladies cardiovasculaires. Le projet comprend la modélisation et la caractérisation des interactions protéine-protéine au sein des sous-domaines des complexes NOX, grâce à des techniques de modélisation de pointe (à l'échelle atomique ou gros grains). Ceci permettra de concevoir des peptides inhibiteurs capables de cibler spécifiquement ces interfaces. Le projet est mené au sein d'un consortium multidisciplinaire impliquant des équipes expérimentales qui synthétiseront et testeront les composés conçus. Les retours de nos collaborateurs expérimentaux contribueront à optimiser l'efficacité des inhibiteurs conçus durant la thèse. Inflammatory syndromes, dementia and cardiovascular diseases remain unresolved challenges for biomedical research. All these conditions have as a common biochemical trait oxidative stress, which is the uncontrolled generation of reactive oxygen species (ROS), oxygen-rich molecules that react with and damage proteins, lipids and nucleic acids. NADPH oxidases (NOXs, see Fig.1) are a major source of cellular ROS and the dysregulation of their enzymatic activity drives numerous pathologies(1,2,3). Despite their recognized importance for human health, there are currently no approved drugs that target NOXs directly.
Our goal is to design a novel class of drugs for the treatment of inflammatory, neurodegenerative and cardiovascular conditions that will directly target the activity of NOX enzymes. NOX activity depends on the formation of an enzymatically active complex that includes membrane-bound enzymatic subunits and regulatory subunits translocating from the cytoplasm to the membrane.4 Peptides interfering with the protein-protein interaction (PPIs) that stabilise the enzymatically active complex have been shown to inhibit NOXs in vitro(5,6), but their adoption for clinical purposes has been limited by their poor pharmacokinetic and immunogenic properties.
In a recent work(7), SSM and AT determined the molecular binding between components of the NOX2 complex using AI-coupled in silico simulations (i.e. Nox2 and p47phox, Fig. 2). A similar strategy can be applied to design peptides disrupting the protein-protein interactions responsible for the complex stabilisation and enzymatic activation of selected NOX isoenzymes. We will apply in silico molecular modeling to: 1) characterize the subunits interactions required for NOX active complex formation 2) identify peptides that inhibit NOXs by interfering with their active enzymatic complex assembly 3) structurally modify them to obtain peptidomimetic compounds, which are small molecules combining the biological effect of peptides with superior pharmacokinetic properties (e.g. absorption, stability and membrane permeability). This last step will benefit from the feedback of our experimental collaborators and will lead to several successive generations of peptidomimetic inhibitors. Objective 1: Molecular modelling of protein-protein interactions required for NOX active complex formation and design of inhibitory peptides.
We will build on the successful strategy developed in a prior study on NOX2 to generate an activation model for NOX1 and NOX4. This will require using AI (such as AF2) and docking tools (such as the HADDOCK suite), to obtain initial structures for the NOX complexes, which will be used as starting points for long-term all-atom Molecular Dynamics (MD) simulations.While AF2 can provide us with an initial global template for the NOX1 and NOX4 assemblies, it usually fails at properly modeling the disordered linkers connecting the globular subdomains of the complex (8). Therefore, a first refinement of the modeled complex structure will likely be needed to eliminate potential steric issues and make a sound starting point for the MD simulations that follow. A second refinement step will be essential for a proper characterization of the interactions between the various subunits composing each complex, as these systems are highly dynamic(9). For NOX1 and NOX2, we will need to investigate how these interfaces evolve during the transition from the inactive to the active state. The analysis of the MD trajectories will give a detailed picture of the inter-protein contacts at the atomic level, permitting the identification of epitopes that are critical for the interactions between the subunits, and specific for each complex.
Objective 2: Molecular modeling-assisted design of inhibitory peptidomimetic compounds.
In the second phase, we will use molecular modeling tools to investigate the impact of targeted local modifications, such as single amino acid substitutions or the introduction of peptidomimetic residues. Notably, parameters for non-natural residues are now available in recent force-field simulators such as CHARMM36, which also predict the stability of the interaction between the peptidomimetics and its protein partner. The goal here is to strengthen the peptide/protein interaction, but also to enhance its membrane permeability, stability, specificity for NOXs, and selectivity for the chosen isoenzyme among NOXs. Again, this will require running MD simulations to calculate binding free energies between the peptide and protein partners. We will monitor the stability of the interaction, both from the structural point of view with classic metrics (such as the fraction of native contacts in the interface along time), and from a thermodynamic perspective, by computing the peptide/protein binding enthalpies and their variation when changing the peptide sequence, using state of the art methodologies such as the alchemical free-energy computation approaches that are currently in use at the LBT(10)

L'étudiant(e) doit être titulaire d'un master en (bio)physique ou en chimie physique et posséder une expérience en modélisation moléculaire. Il/Elle doit manifester un intérêt pour la modélisation de systèmes biologiques complexes et être capable de travailler à différentes échelles avec une gamme d'outils variés.