Investigating the promising SARS-CoV-2 main protease inhibitory activity of secoiridoids isolated from ; and assessments with structure-activity relationship.

The proteolytic enzyme 3 C-like protease (3Clpro or M) is considered the most important target for SARS-CoV-2 which could be attributed to its crucial role in viral maturation and/or replication. Besides, natural phytoconstituents from plant origin are always promising lead compounds in the drug discovery area. Herein, the previously isolated and identified seven compounds from () were examined and against the SARS-CoV-2 M. First, the Vero E6 cells were utilized to pursue the potential of the investigated compounds (both in fractions and individual isolates) using the MTT assay. The total extract () displayed the most significant activity against SARS-CoV-2 with IC = 29.36 µg/mL. Besides, the fractions ( and ) showed good activity against the SARS-CoV-2 with IC values of 70.42, and 73.09 µg/mL, respectively. Then, the SARS-CoV-2 M inhibitory assay was utilized to emphasize the inhibitory potential of the investigated isolates. , , and candidates displayed prominent M inhibitory potentials with IC = 30.44, 30.24, and 56.25 µM, respectively. Moreover, molecular docking of the identified seven compounds against the M of SARS-CoV-2 showed that the five secoiridoids achieved superior results. , , , and showed higher affinities towards the M target compared to the co-crystallized antagonist. Furthermore, the most active complexes (, , , and ) were subjected to MD simulations run for 150 ns and MM-GBSA calculations, compared to the co-crystallized inhibitor (). Finally, the SAR study clarified that achieved the best anti-SARS-CoV-2 M activity followed by .Communicated by Ramaswamy H. Sarma.