Biology subjects

Ferraz, M.

Publications and source records attributed to Ferraz, M..

3 recordsLinked to original sources

bioRxiv2026

Glycosylation of anandamide and other bioactive N-acylethanolamines in mammalian cells and tissues

N-acylethanolamines (NAEs), including the endocannabinoid anandamide, are bioactive fatty acid amides that are normally hydrolyzed by fatty acid amide hydrolase (FAAH) or N-acyl acid amidohydrolase (NAAA). Strikingly, when canonical NAE degradation is blocked, NAE levels do not increase indefinitely but instead reach a plateau. This apparent metabolic ceiling suggests that additional, underexplored pathways contribute to NAE homeostasis. Identifying these pathways is essential to determine whether NAEs are converted into inactive metabolites or products with distinct biological properties. Here, we identify NAE glycosylation as a metabolic pathway that links endocannabinoid-related lipid metabolism to glycosphingolipid turnover. We synthesized glycosylated NAEs and their isotope-encoded standards and developed targeted LC-MS/MS assays to monitor their enzymatic processing and quantify their abundance in mouse and human cells, tissues, and plasma. We show that non-lysosomal glucosylceramidase GBA2 transfers glucose or galactose to anandamide, N-oleoylethanolamine and N-palmitoylethanolamine, and lysosomal glucosylceramidase GCase hydrolyses {beta}-Glycosylated-NAEs ({beta}-Glyco-NAE) back to their parent NAEs. {beta}-Glyco-NAEs occur endogenously in macrophages and neuronal cells, increase when canonical NAE degradation is impaired, and accumulate in human samples with GCase deficiency, including Gaucher disease and GBA1-associated Parkinsons disease. {beta}-Glyco-NAEs do not engage the cannabinoid receptors, TRPV1, or PPAR, and potentiate inflammatory cytokine release, including IL6 and TNF, from microglia. Based on these findings, we pose that GBA2-dependent NAE glycosylation may constitute an overflow lipid-remodeling pathway that connects NAE metabolism to lysosomal dysfunction, inflammation and neurodegeneration.

biochemistry↗

bioRxiv2026

Generative AI Guided Design of High-Affinity T cell Receptors

Developing T cell receptors (TCRs) with sufficiently high affinity for tumor antigens (TAs) remains a fundamental challenge in TCR-T immunotherapy. Experimental methods such as affinity maturation and high-throughput screening have enabled the identification of TCRs with enhanced activity. However, their efficiency is often constrained by limited throughput, insufficient coverage, and the generally lower affinities of naturally occurring TCRs toward TAs. To address these challenges, we present TCRPPO2, an integrated AI-driven, in silico affinity maturation framework for peptide-specific TCR optimization. Using reinforcement learning, TCRPPO2 learns mutation policies that iteratively enhance the TCR binding affinity to the target peptide, derived from predictive models trained on carefully curated interaction data. The model is further augmented by a generative AI critic model that discourages implausible designs to ensure the biophysical validity. The designs are further screened by robust post-screening methods that leverage diverse functional annotations and physical prior knowledge. We applied TCRPPO2 to the clinically relevant MART-1 antigen and experimentally validated the designed candidates in Jurkat cell-based functional assays. Among the five engineered TCRs, all of which demonstrated positive cellular responses, three showed significantly increased activities relative to their templates and one showed substantial enhancement. These functional gains were consistent with more favorable interaction energy from structural and physical modeling. Together, our results support a generalizable paradigm for TCR engineering, in which learned mutation policies can efficiently navigate the peptide-specific binding landscape of TCRs and propose biologically enhanced candidates without explicit structural supervision, offering a practical route for early-stage computational TCR optimization for challenging tumor antigens.

immunology↗

bioRxiv2024

The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming

Although it is well established that the SARS-CoV-2 spike glycoprotein binds to the host cell ACE2 receptor to initiate infection, far less is known about the tissue tropism and host cell susceptibility to the virus. Differential expression across different cell types of heparan sulfate (HS) proteoglycans, with variably sulfated glycosaminoglycans (GAGs), and their synergistic interactions with host and viral N-glycans may contribute to tissue tropism and host cell susceptibility. Nevertheless, their contribution remains unclear since HS and N-glycans evade experimental characterization. We, therefore, carried out microsecond-long all-atom molecular dynamics simulations, followed by random acceleration molecular dynamics simulations, of the fully glycosylated spike:ACE2 complex with and without highly sulfated GAG chains bound. By considering the model GAGs as surrogates for the highly sulfated HS expressed in lung cells, we identified key novel cell entry mechanisms of spike SARS-CoV-2. We find that HS promotes structural and energetic stabilization of the active conformation of the spike receptor binding domain (RBD) and reorientation of ACE2 toward the N-terminal domain in the same spike subunit as the RBD. Spike and ACE2 N-glycans exert synergistic effects, promoting better packing, strengthening the protein:protein interaction, and prolonging the residence time of the complex. ACE2 and HS binding trigger rearrangement of the S2 functional protease cleavage site through allosteric interdomain communication. These results thus show that HS has a multifaceted role in facilitating SARS-CoV-2 infection and they provide a mechanistic basis for the development of novel GAG derivatives with anti-SARS-CoV-2 potential. Significance StatementA key to blocking SARS-CoV-2 infection is to understand why it infects some cell types more than others. Heparan sulfate (HS) proteoglycans are differentially expressed on the surface of host cells and, with ACE2 receptors, provide an entry route for SARS-CoV-2. Here, we used computer simulations to investigate how highly sulfated glycosaminoglycans, a model for HS expressed in lungs, impact the interaction between virus spike and host ACE2. The simulations indicate that HS, together with host and spike N-glycans, stabilizes the spike:ACE2 complex and triggers structural changes, including host protease cleavage, contributing to the SARS-CoV-2 infection mechanism. This study lays the basis for a better understanding of the cell-specificity of SARS-CoV-2 infection and for developing strategies for inhibiting SARS-CoV-2 infection.

biophysics↗