Comprehensive structural and functional analysis of Patuletin as a potent inhibitor of SARS-CoV-2 targeting the RNA-dependent RNA polymerases

Abstract

In the pursuit of identifying effective inhibitors against SARS-CoV-2, we conducted a detailed investigation into the binding interactions and inhibitory potential of Patuletin targeting the RNA-Dependent RNA Polymerase (RdRp), comparing it with the well-known anti-RdRp agent, Remdesivir. Superimposition molecular docking studies uncovered a high degree of similarity in binding modes between Patuletin and Remdesivir within the active site of the RdRp. MD simulations (RMSD, RMSF, RG, SASA, hydrogen bonding) over a 200 ns trajectory provided valuable insights into the binding and interactions of Patuletin and RdRp comparing Remdesivir. These simulations validated the correct binding and optimum changes in both energetic and dynamic aspects, confirming the stability of the Patuletin-RdRp complex comparing the Remdesivir-RdRp complex. Further, the MM-GBSA technique revealed favorable binding energies, with Patuletin displaying a significantly lower value (-4.24 kcal/mol) compared to Remdesivir (-2.15 kcal/mol), affirming the robustness of Patuletin-RdRp binding. The MM-GBSA analysis additionally examined the binding energetic components, revealing a high degree of similarity between Patuletin and Remdesivir. 3D binding interactions were investigated through ProLIF and PLIP studies reinforcing the stable binding observed in the simulations. Principal component analysis of trajectories (PCAT) studies were employed to discern coordinated motions within the evaluated systems, providing additional perspectives on the dynamic behavior of the Patuletin-RdRp complex. In vitro assays demonstrated Patuletin's exceptional inhibitory potency against the RdRp, with an IC50 of 248 nM, far surpassing Remdesivir, which exhibited an IC50 of 20 µM. Interestingly, the in vitro IC50 against SARS-CoV-2 values further supported the superior efficacy of Patuletin (0.476 µg/ml) over Remdesivir (10.86 µg/ml). Furthermore, the viral selectivity index (SI) values highlighted the remarkable safety margin of Patuletin (SI: 790.76) compared to Remdesivir (SI: 5.87), underscoring the potential of Patuletin as a safer and more potent therapeutic agent against SARS-CoV-2. In conclusion, our comprehensive analysis presents Patuletin as a promising candidate for further exploration as a potent inhibitor of SARS-CoV-2 RdRp, offering valuable insights for the development of effective anti-COVID-19 therapies.