scholarly journals Antiviral Activity of Metabolites from Peruvian Plants against SARS-CoV-2: An In Silico Approach

Molecules ◽  
2021 ◽  
Vol 26 (13) ◽  
pp. 3882
Author(s):  
Luis Daniel Goyzueta-Mamani ◽  
Haruna Luz Barazorda-Ccahuana ◽  
Karel Mena-Ulecia ◽  
Miguel Angel Chávez-Fumagalli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
High Stability ◽  
Native Plants ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Pharmacological Properties ◽  
Potential Candidate ◽  
In Silico Screening

(1) Background: The COVID-19 pandemic lacks treatments; for this reason, the search for potential compounds against therapeutic targets is still necessary. Bioinformatics tools have allowed the rapid in silico screening of possible new metabolite candidates from natural resources or repurposing known ones. Thus, in this work, we aimed to select phytochemical candidates from Peruvian plants with antiviral potential against three therapeutical targets of SARS-CoV-2. (2) Methods: We applied in silico technics, such as virtual screening, molecular docking, molecular dynamics simulation, and MM/GBSA estimation. (3) Results: Rutin, a compound present in Peruvian native plants, showed affinity against three targets of SARS-CoV-2. The molecular dynamics simulation demonstrated the high stability of receptor–ligand systems during the time of the simulation. Our results showed that the Mpro-Rutin system exhibited higher binding free energy than PLpro-Rutin and N-Rutin systems through MM/GBSA analysis. (4) Conclusions: Our study provides insight on natural metabolites from Peruvian plants with therapeutical potential. We found Rutin as a potential candidate with multiple pharmacological properties against SARS-CoV-2.

scholarly journals In Silico Screening, Genotyping, Molecular Dynamics Simulation and Activity Studies of SNPs in Pyruvate Kinase M2

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0120469 ◽  
Author(s):  
Ponnusamy Kalaiarasan ◽  
Bhupender Kumar ◽  
Rupali Chopra ◽  
Vibhor Gupta ◽  
Naidu Subbarao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Pyruvate Kinase ◽  
In Silico ◽  
Dynamics Simulation ◽  
In Silico Screening ◽  
Pyruvate Kinase M2

scholarly journals Structure-based virtual screening suggests inhibitors of 3-Chymotrypsin-Like Protease of SARS-CoV-2 from Vernonia amygdalina and Occinum gratissimum

2021 ◽  
Author(s):  
Gideon A. Gyebi ◽  
Abdo A. Elfiky ◽  
Oludare M. Ogunyemi ◽  
Ibrahim M. Ibrahim ◽  
Adegbenro P. Adegunloye ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
In Silico ◽  
Hydrophobic Interactions ◽  
Binding Free Energy ◽  
Intermediate Formation ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Vernonia Amygdalina

Abstract An in-house library of 173 phytocompound structures from Vernonia amygdalina and Occinum gratissimum was screened against the active region of 3-Chymotrypsin-Like Protease (3CLpro) of SARS-CoV-2 in silico. Based on docking scores and reference inhibitors, a hit- list of 21 phytocompounds, with binding energies ranging from − 7.2 to -8.0 kcal/mol, was initially generated. Further docking against the 3CLpro of related coronaviruses (SARS-CoV and MERS-CoV), docking to 5 different representative conformations generated from the cluster analysis of SARS-CoV-2 3CLpro molecular dynamics simulation (MDS) trajectories, and in silico drug-likeness analyses, revealed two drug-like terpenoid structures as promising non-covalent inhibitors of SARS-CoV-2 3CLPro viz: neoandrographolide and vernolide. These terpenoid structures are accommodated within the substrate-binding pocket, and interacted with the catalytic dyad, the oxyanion loop (residues 138–145), and the S1/S2 subsites of the enzyme active site. With the aid of an array of hydrogen bonds and hydrophobic interactions with residues 142–145, these phytocompounds may stabilize the conformation of the flexible oxyanion loop; and thereby interfere with the tetrahedral oxyanion intermediate formation during proteolytic cleavage. Molecular dynamics simulation and binding free energy calculation further revealed that the terpenoid-enzyme complexes exhibit strong interactions and structural stability, which could be adapted for experimental models.

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