Original article
Benchmarked molecular docking integrated molecular dynamics stability analysis for prediction of SARS-CoV-2 papain-like protease inhibition by olive secoiridoids

https://doi.org/10.1016/j.jksus.2022.102402Get rights and content
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Abstract

Objectives

We performed a virtual screening of olive secoiridoids of the OliveNetTM library to predict SARS-CoV-2 PLpro inhibition. Benchmarked molecular docking protocol that evaluated the performance of two docking programs was applied to execute virtual screening. Molecular dynamics stability analysis of the top-ranked olive secoiridoid docked to PLpro was also carried out.

Methods

Benchmarking virtual screening used two freely available docking programs, AutoDock Vina 1.1.2. and AutoDock 4.2.1. for molecular docking of olive secoiridoids to a single PLpro structure. Screening also included benchmark structures of known active and decoy molecules from the DEKOIS 2.0 library. Based on the predicted binding energies, the docking programs ranked the screened molecules. We applied the usual performance evaluation metrices to evaluate the docking programs using the predicted ranks. Molecular dynamics of the top-ranked olive secoiridoid bound to PLpro and computation of MM-GBSA energy using three iterations during the last 50 ps of the analysis of the dynamics in Desmond supported the stability prediction.

Results and discussions

Predictiveness curves suggested that AutoDock Vina has a better predictive ability than AutoDock, although there was a moderate correlation between the active molecules rankings (Kendall's correlation of rank (τ) = 0.581). Interestingly, two same molecules, Demethyloleuropein aglycone, and Oleuroside enriched the top 1 % ranked olive secoiridoids predicted by both programs. Demethyloleuropein aglycone bound to PLpro obtained by docking in AutoDock Vina when analyzed for stability by molecular dynamics simulation for 50 ns displayed an RMSD, RMSF<2 Å, and MM-GBSA energy of −94.54 ± 6.05 kcal/mol indicating good stability. Molecular dynamics also revealed the interactions of Demethyloleuropein aglycone with binding sites 2 and 3 of PLpro, suggesting a potent inhibition. In addition, for 98 % of the simulation time, two phenolic hydroxy groups of Demethyloleuropein aglycone maintained two hydrogen bonds with Asp302 of PLpro, specifying the significance of the groups in receptor binding.

Conclusion

AutoDock Vina retrieved the active molecules accurately and predicted Demethyloleuropein aglycone as the best inhibitor of PLpro. The Arabian diet consisting of olive products rich in secoiridoids benefits from the PLpro inhibition property and reduces the risk of viral infection.

Abbreviations

AD
AutoDock 4.2.1
ADV
AutoDock Vina 1.1.2
DEKOIS
Demanding evaluation kits for objective in-silico screening
EF
Enrichment factor
g/mol
Grams/mole
kcal/mol
Kilocalorie/mole
MD
Molecular dynamics
MM-GBSA
Molecular mechanics generalized Born surface area
MW
Molecular weight
M
Moles
ns
nanoseconds
OS
Olive secoiridoids
PLpro
Papain-like protease
ps
picoseconds
RMSD
Root mean square deviation
RMSF
Root mean square fluctuation
ROC
Receiver operating characteristic curve
ROC-AUC
Area under ROC
pAUC
partial area under ROC
BEDROC
Boltzmann enhanced discrimination of ROC
RIE
Robust initial enhancement
pTG
Partial total gain
PC
Predictiveness curve
SARS-CoV-2
Severe acute respiratory syndrome coronavirus-2
TG
Total gain

Keywords

Benchmarking docking
Molecular docking
Molecular dynamics
Olive secoiridoids
PLpro
SARS-CoV-2

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Peer review under responsibility of King Saud University.