Laurent Chaloin

Neurodevelopmental conditions, including attention deficit hyperactivity disorder (ADHD) and autism spectrum disorders (ASD), have increased markedly over recent decades. This rise parallels the widespread use of agrochemicals, suggesting a contribution of environme ntal exposures. We hypothesize that pesticide residues may disrupt brain development and promote neurodevelopmental disorders. Here, we test whether concentrations permitted in drinking water affect brain development using a maternal exposure model in wild-type mice. Exposure to a fungicide mixture at 0.3 µg/L, below the current European regulatory limit of 0.5 µg/L, impairs corticogenesis and is associated with alterations in synaptic function and glutamate rgic signaling. Offspring exhibit delays in sensory development, reduced social interactions, and increased stereotyped behaviors. We identify the adenosine A2A receptor as a molecular target of anilinopyrimidine fungicides. Together, these findings indicate that low-dose exposure to this fungicide mixture can induce an autism spectrum-like phenotype in the offspring.

Despite its efficiency to prevent viral multiplication, antiretroviral therapy does not affect HIV-1 latently-infected cells. These cells do not produce significant amounts of viruses and constitute HIV-1 reservoir. To purge this long-lived viral reservoir, the "shock and kill" strategy relies on the use of latency reversing agents (LRAs) to induce activation of latent cells. All LRAs developed until now target cellular proteins and are therefore not specific for HIV-infected cells. Here we present a new LRA that binds and activates HIV-1 Tat which is the key regulator for viral transcription and latency reversal. This molecule termed D10 was designed to bind to the major groove of the Tat protein, and found to activate Tat transcriptional activity by stabilizing the HIV transcription complex. This LRA induces strong HIV production by latent cell lines and latent cells from people living with HIV-1. On latent cells from PBMCs, D10 is active at ∼50 nM, the concentration required to stabilize HIV transcription complex. D10 is the first Tat activator available and the first LRA that targets an HIV protein.

The Syk tyrosine kinase acts downstream of several immune receptors such as the FcγR. Syk owns two SH2 domains that interact with biphosphorylated ITAMs of the FcγR upon phagocytosis. This results in the activation of Syk by autophosphorylation, triggering phosphorylation of several downstream targets, F-actin polymerization, and phagocytosis of the IgG-opsonized target. We found that Syk is S-acylated upon phagocytosis by macrophages. Palmitoylation is performed on a single Syk-Cys by the DHHC5 enzyme that specifically associates with Syk upon phagocytosis. Syk palmitoylation is important for Syk localization to the phagocytic cup, phosphorylation, and phagocytosis. We observed that another Syk-Cys residue, within a redox motif, is modified by sulfenylation. Nevertheless, Syk desulfenylation seems to occur during phagocytosis, when H ₂ O ₂ production at the cup decreases, after 3.5 min of phagocytosis. Molecular dynamics studies indicated that desulfenylation increased the exposure of a loop within the Syk interdomain B. This could facilitate phosphorylation of key Syk-Tyr residues by upstream kinases. We thus propose an updated model for Syk activation during FcγR-mediated phagocytosis that involves both Syk palmitoylation and desulfenylation.

The non-receptor Spleen tyrosine kinase Syk acts downstream of several receptors of the immune system such as the FcγR. Syk is composed of a kinase domain and two SH2 domains that interact with the bi- phosphorylated ITAMs motifs of the FcγR upon phagocytosis. This results in the activation of Syk by auto- phosphorylation, triggering phosphorylation of several downstream targets in a process that will culminate in F-actin polymerization and phagocytosis of the IgG-opsonized target. We found that Syk is S-acylated upon phagocytosis by macrophages. Palmitoylation is performed on a single Syk-Cys by the protein S-acyl transferase DHHC5 that specifically associates with Syk upon phagocytosis. Syk palmitoylation is required for Syk localization to the phagocytic cup, Syk phosphorylation/activation, Cdc42 recruitment to the cup, F-actin polymerization and phagocytosis. We also observed that another Syk-Cys residue is modified by sulfenylation. Mutation of the sulfenylated Cys that belongs to a redox-motif inactivated the Syk catalytic activity and phagocytosis. We found that Syk desulfenylation occurs during phagocytosis. Molecular dynamics studies indicated that desulfenylation increased the mobility and exposure of a loop within the Syk interdomain B, likely facilitating phosphorylation of key Syk-Tyr residues by upstream effectors such as Src kinases. We thus propose an original updated model for Syk activation during FcγR-mediated phagocytosis that involves both Syk palmitoylation and desulfenylation.

The SARS-CoV-2 spike protein binds to the angiotensin-converting enzyme 2 (ACE2) receptor to mediate viral entry, with mutations in different variants influencing binding affinity and conformational dynamics. Using large-scale molecular dynamics simulations, we analyzed the Spike–ACE2 complex in the wild-type (WT), Beta, and Delta variants. Our findings reveal significant conformational rearrangements at the inter-face in Beta and Delta compared to WT, leading to distinct interaction networks and changes in complex stability. Binding free energy analysis further highlights variant-specific differences in ACE2 affinity, with alternative binding modes emerging over the simulation. The results enhance our understanding of spike–ACE2 stoichiometry across variants, providing implications for viral infectivity and therapeutic targeting.

The SARS-CoV-2 Omicron variants show different behavior compared to the previous variants, especially with respect to the Delta variant, which promotes a lower morbidity despite being much more contagious. In this perspective, we performed molecular dynamics (MD) simulations of the different spike RBD/hACE2 complexes corresponding to the WT, Delta and four Omicron variants. Carrying out a comprehensive analysis of residue interactions within and between the two partners allowed us to draw the profile of each variant by using complementary methods (PairInt, hydrophobic potential, contact PCA). PairInt calculations highlighted the residues most involved in electrostatic interactions, which make a strong contribution to the binding with highly stable interactions between spike RBD and hACE2. Apolar contacts made a substantial and complementary contribution in Omicron with the detection of two hydrophobic patches. Contact networks and cross-correlation matrices were able to detect subtle changes at point mutations as the S375F mutation occurring in all Omicron variants, which is likely to confer an advantage in binding stability. This study brings new highlights on the dynamic binding of spike RBD to hACE2, which may explain the final persistence of Omicron over Delta.

Aminoglycoside‐phosphotransferases (APHs) are a class of bacterial enzymes that mediate acquired resistance to aminoglycoside antibiotics. Here we report the identification of small molecules counteracting aminoglycoside resistance in Enterococcus casseliflavus. Molecular dynamics simulations were performed to identify an allosteric pocket in three APH enzymes belonging to 3′ and 2′′ subfamilies in which we then screened, in silico, 12,000 small molecules. From a subset of only 14 high‐scored molecules tested in vitro, we identified a compound, named here EK3, able to non‐competitively inhibit the APH(2′′)‐IVa, an enzyme mediating clinical gentamicin resistance. Structure‐activity relationship (SAR) exploration of this hit compound allowed us to identify a molecule with improved enzymatic inhibition. By measuring bacterial sensitivity, we found that the three best compounds in this series restored bactericidal activity of various aminoglycosides, including gentamicin, without exhibiting toxicity to HeLa cells. This work not only provides a basis to fight aminoglycoside resistance but also highlights a proof‐of‐concept for the search of allosteric modulators by using in silico methods.

The SARS-CoV-2 Omicron variants present a different behavior compared to the previous variants, all particularly in respect to the Delta variant, as it seems to promote a lower morbidity although being much more contagious. In this perspective, we performed new molecular dynamics (MD) simulations of the various spike RBD/hACE2 complexes corresponding to the WT, Delta and Omicron variants (BA.1 up to BA.4/5) over 1.5 µs timescale. Then, carrying out a comprehensive analysis of residue interactions within and between the two partners, allowed us to draw the profile of each variant by using complementary methods (PairInt, hydrophobic potential, contact PCA). Main results of PairInt calculations highlighted the most involved residues in electrostatic interactions that represent a strong contribution in the binding with highly stable contacts between spike RBD and hACE2 (importance of mutated residues at positions 417, 493 and 498). In addition to the swappable arginine residues (493/498), the apolar contacts made a substantial and complementary contribution in Omicron with the detection of two hydrophobic patches, one of which was correlated with energetic contribution calculations. This study brings new highlights on the global dynamics of spike RBD/hACE2 complexes resulting from the analysis of contact networks and cross-correlation matrices able to detect subtle changes at point mutations. The results of our study are also consistent with alternative approaches such as binding free energy calculations but are more informative and sensitive to transient or low-energy interactions. Nevertheless, the energetic contributions of residues at positions 501 and 505 were in good agreement with hydrophobic interactions measurements. The contact PCA networks could identify the intramolecular incidence of the S375F mutation occurring in all Omicron variants and likely conferring them an advantage in binding stability. Collectively, these data revealed the major differences observed between WT/Delta and Omicron variants at the RBD/hACE2 interface, which may explain the greater persistence of Omicron. Author Summary: The evolution of SARS-CoV-2 was extremely rapid, leading to the global predominance of Omicron variants, despite the many mutations identified in the spike protein. Some of these were introduced to evade the immune system, but many others were located in the Receptor Binding Domain (RBD) without affecting its efficient binding to hACE2 and preserving the high infectivity of this variant. To unravel the mechanism by which this protein-protein connection remains strong or stable, it is necessary to study the different types of interactions at the atomic level and over time using molecular dynamics (MD) simulations. Indeed, in contrast to crystal or cryo-EM structures providing only a fixed image of the binding process, MD simulations have allowed to unambiguously identify the sustainability of some interactions mediated by key residues of spike RBD. This study could also highlight the interchangeable role of certain residues in compensating for a mutation, which in turn allows the virus to maintain durable binding to the host cell receptor. Graphical

HIV-1 capsids cross nuclear pore complexes (NPCs) by engaging with the nuclear import machinery. To identify compounds that inhibit HIV-1 nuclear import, we screened drugs in silico on a three-dimensional model of a CA hexamer bound by Transportin-1 (TRN-1). Among hits, compound H27 inhibited HIV-1 with a low micromolar IC ₅₀ . Unlike other CA-targeting compounds, H27 did not alter CA assembly or disassembly, inhibited nuclear import specifically, and retained antiviral activity against PF74- and Lenacapavir-resistant mutants. The differential sensitivity of divergent primate lentiviral capsids, capsid stability and H27 escape mutants, together with structural analyses, suggest that H27 makes multiple low affinity contacts with assembled capsid. Interaction experiments indicate that H27 may act by preventing CA from engaging with components of the NPC machinery such as TRN-1. H27 exhibited good metabolic stability in vivo and was efficient against different subtypes and circulating recombinant forms from treatment-naïve patients as well as strains resistant to the four main classes of antiretroviral drugs. This work identifies compounds that demonstrate a novel mechanism of action by specifically blocking HIV-1 nuclear import.