Biology subjects

Cosconati, S.

Publications and source records attributed to Cosconati, S..

4 recordsLinked to original sources

bioRxiv2026

Targeting the Tumor-Stroma Crosstalk: An AI-Based Virtual Screening Strategy for Dual MET/SMO Inhibitors in Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy characterized by a dense desmoplastic tumor microenvironment (TME) that limits drug penetration and promotes immune evasion. Effective treatment, therefore, requires simultaneous modulation of multiple signaling pathways. Here, we describe a directed polypharmacological strategy to identify dual modulators of c-MET and Smoothened (SMO), aiming to disrupt the protective stroma through SMO inhibition while directly suppressing tumor cell survival via c-MET targeting. An AI-guided virtual screening workflow combining the machine-learning platform PyRMD, trained on known c-MET and SMO ligands, with structure-based molecular docking was applied to a library of over 9 million compounds. This approach led to the identification of compound 21, an aminopyrimidine-benzamide-phenoxyquinoline derivative, as a dual c-MET/SMO inhibitor. Biochemical and cellular studies demonstrated that compound 21 selectively binds the SMO orthosteric site (pKi = 5.60), inhibits agonist-induced GLI (Glioma-associated oncogene) signaling (pIC50 = 5.50), and potently suppresses c-MET kinase activity (pIC50 = 6.94). Western blot analyses further revealed that compound 21 promotes ubiquitin-proteasome-mediated degradation of c-MET, eliminating receptor availability and limiting compensatory resistance signaling. In 3D heterotypic models comprising MIAPaCa2 pancreatic cancer cells and CAF154-hTERT fibroblasts, dual inhibition of SMO-mediated stromal support and c-MET-driven tumor progression resulted in greater cytotoxicity than the combination of the selective inhibitors Sonidegib and PHA-665752. Overall, compound 21 overcomes stromal-mediated resistance, enhances tumor cell death, and validates dual SMO/c-MET targeting as a promising single-agent therapeutic strategy for PDAC. One Sentence SummaryAn AI-identified dual SMO/c-MET inhibitor overcomes stromal resistance and degrades c-MET to suppress pancreatic cancer.

cancer biology↗

bioRxiv2026

AI-Enforced Ultra-Large Virtual Screening Discovers Potent CD28 Binders

Targeting protein-protein interactions (PPIs) with small molecules is historically challenging due to shallow, solvent-exposed interfaces that lack classical binding pockets. Furthermore, employing traditional structure-based virtual screening (SBVS) across ultra-large chemical spaces to find novel chemotypes imposes prohibitive computational bottlenecks. Here, we report the first prospective, real-world application of the PyRMD2Dock platform, an AI-enforced SBVS workflow that integrates machine learning and standard docking available within the PyRMD Studio suite. To target the structurally demanding immune receptor CD28, a chemically diverse subset of 2.4 million molecules from the Enamine REAL Diversity Space was docked into a cleft adjacent to the canonical ligand interface. These data were used to train 672 classification models, and the optimized model rapidly screened the remaining [~]46 million compounds. Following interaction filtering and clustering, 232 highly prioritized ligands were identified. Experimental validation of 150 purchased candidates yielded a remarkable hit rate, identifying multiple direct CD28 binders. Lead compounds 100 and 104 exhibited submicromolar affinity (Kd = 343.8 nM and 407.1 nM, respectively), potent CD28-CD80 disruption, and functional blockade in cellular reporter assays. Furthermore, these compounds successfully reduced cytokine secretion in primary human tumor-PBMC and epithelial tissue co-culture models. This study validates PyRMD2Dock as a highly scalable, effective protocol for mining massive chemical libraries to discover small-molecule modulators of challenging immune receptor interfaces.

pharmacology and toxicology↗

bioRxiv2025

AI-Driven Virtual Screening and First-in-Class Conformational Biosensor Enable the Discovery of a GPR183 Inverse Agonist

GPR183 is a chemotactic G protein-coupled receptor implicated in immune cell migration and various diseases. Here, we report the discovery of novel GPR183 inverse agonists using an artificial intelligence-driven virtual screening approach combined with biophysical sensors including a first-in-class conformational biosensor. From an initial screen of 70 compounds and a hit expansion, a selected candidate - compound 78 - demonstrated potent inhibition of GPR183s constitutive and agonist-stimulated Gi activation as well {beta}-arrestin2 recruitment. The binding of the compound to the receptor core was confirmed by studies using a new conformational sensor based on intramolecular BRET, molecular dynamics, and site-directed mutagenesis experiments. Finally, the compound 78 was able to block agonist-induced migration of peripheral blood mononuclear cells ex vivo. This work provides a novel chemical scaffold for GPR183 modulation. It introduces a new tool for dissecting receptor function, paving the way for therapeutic exploration in inflammatory, autoimmune, and neoplastic disorders.

pharmacology and toxicology↗

bioRxiv2023

Irreversible inhibition of TRF2TRFH recruiting functions: a strategy to induce telomeric replication stress in cancer cells.

The shelterin component telomeric repeat-binding factor 2 (TRF2) is an essential regulator of telomere homeostasis and genomic stability. Mutations in the TRF2TRFH domain physically impair t-loop formation and prevent the recruitment of several factors that promote efficient telomere replication, resulting in a telomeric DNA damage response. Here, we design, synthesize, and biologically test covalent cyclic peptides that irreversibly target the TRF2TRFH domain. We identify APOD53 as our most promising compound. APOD53 forms a covalent adduct with a reactive cysteine residue present in the TRF2TRFH domain and induces phenotypes consistent with TRF2TRFH domain mutants. These include induction of a telomeric DNA damage response in the absence of fusions, increased telomeric replication stress, and impaired recruitment of regulator of telomere elongation helicase 1 (RTEL1) and structure-specific endonuclease subunit (SLX4) to telomeres. We demonstrate that APOD53 impairs cell growth in both a telomerase-positive and an ALT cell line, while sparing the viability of non-cancerous cells. Finally, we find that co-treatment with APOD53 and the G4 stabilizer RHPS4 further exacerbates telomere replication stress.

cancer biology↗