The chiral 5,6-cyclohexane-fused uracil ring-system: A molecular platform with promising activity against SARS-CoV-2

• DOI: 10.1016/j.ejmech.2025.117302
• Publication Date: 2025-01-21T08:29:16Z
• Authors: Enrico Marcantonio; Debora Guazzetti; Crescenzo Coppa; Lucia Battistini; Andrea Sartori; Kelly Bugatti; Becky Provinciael; Claudio Curti; Alessandro Contini; Kurt Vermeire; Franca Zanardi
• Keywords: antiviral docking Molecular Dynamics Nwat-MMGBSA RdRp SARS-CoV-2 tetrahydroquinazoline-2,4-diones; Antiviral; Docking; Molecular dynamics; Nwat-MMGBSA; RdRpSARS-CoV-2; Tetrahydroquinazoline-2,4-diones;; 610; Settore CHEM-05/A - Chimica organica; 540

The recurrent global exposure to highly challenging viral epidemics, and the still limited spectrum of effective pharmacological options step on the accelerator towards the development of new antiviral medicines. In this work we explored the anti-SARS-CoV-2 potential of a recently launched chiral ring system based on the uracil scaffold fused to carbocycle rings. The asymmetric synthesis of two generations of chiral uracil-based compounds (overall 31 different products), and their in vitro cytotoxicity and antiviral screening against wild-type SARS-CoV-2 in U87.ACE cells allowed us to identify seven non-cytotoxic enantioenriched derivatives exhibiting in vitro EC50 in the 6–37 μM range. Among these compounds, bicyclic uracil 10 showed the best antiviral potency against SARS-CoV-2 (EC50 20A.EU2 = 7.41 μM and EC50 Omicron = 19.4 μM), combined with a favourable selectivity index. Additionally, it exhibited single-digit micromolar inhibition of the isolated SARS-CoV-2 RNA-dependent RNA polymerase (IC50 = 2.1 μM). Starting from a reported cryo-EM structure of RdRp, docking and molecular dynamics simulations were performed to rationalize possible binding modes of the active compounds. Interestingly, no inhibition of viral replication in cells was observed against a wide spectrum of human viruses, while some derivatives, and especially hit compound 10, exhibited specific low micromolar antiviral effect against β-coronavirus OC43. Collectively, these data indicate that this novel uracil-based ring system represents a valid starting point for further development of a new class of RdRp inhibitors to treat SARS-CoV-2 and, potentially, other β-coronavirus infections.