Skip to main content
. 2022 Jan 10;14(2):274. doi: 10.3390/nu14020274

Table 4.

Relevant computational methods and bioinformatics tools to research antiviral agents and probiotics against SARS-CoV-2.

No. Aim of Research Computational Methods Tools [Reference of the Tools] Reference
1 Investigate and identify potential hits that could inhibit SARS-CoV-2 by carrying out virtual screening, which included molecular docking, in silico ADMET, and simulation Screened phytochemicals against five protein targets of COVID-19 (3CLpro, RdRp, ACE2, PLpro, SGp-RBD)
Predicted best-docked score phytochemicals in terms of:

  • in silico ADMET prediction

  • Drug-likeness prediction
  • -

    AutoDock Vina [139]

  • -

    pkCSM [148]

  • -

    Molinspiration [149]

 [142]
2 Research the role of tea polyphenols on SARS-CoV-2 inhibition
  • -

    Ligand preparation

  • -

    Binding site prediction

  • -

    Molecular docking

  • -

    Mutagenesis analysis

  • -

    Evaluate the stability of mutant protein structure

  • -

    Molecular dynamics simulation

  • -

    Generate ligand topology files

  • -

    Molecular visualizatio
  • -

    AutoGridFR [150]

  • -

    AutoDock Vina [139]

  • -

    Mutagenesis wizard [151]

  • -

    DynaMut web server [152]

  • -

    CHARMM-GUI web server [153]

  • -

    Visual Molecular Dynamics (VMD) [154]

 [135]
3 Study the interaction of luteolin, ribavirin, chloroquine, and remdesivir with the main protease of COVID-19
  • -

    Molecular docking
  • -

    AutoDock Vina [139]

 [144]
4 Investigate the effects of pomegranate peel extract on SARS-CoV-2 spike glycoproteins, furin, ACE2, and transmembrane serine protease 2
  • -

    Protein active site prediction

  • -

    Molecular docking

  • -

    Analyze the best binding affinity docking positions with a visualization tool
  • -

    DoGSiteScorer [155]

  • -

    AutoDock Vina [139]

  • -

    Discovery Studio [156]

 [143]
5 Investigate the effect of remdesivir, sofosbuvir, ribavirin, galidesivir and tenofovir on RdRp
  • -

    Homology model for RdRp

  • -

    Examining the model

  • -

    Checking the validity of the model

  • -

    Optimizing the model

  • -

    Molecular docking

  • -

    Examining the structure after docking
  • -

    SWISS-MODEL server [157]

  • -

    MolProbity web server [158]

  • -

    PROCHECK [159]; Verify 3D [160]; ERRAT [161]

  • -

    AutoDock Vina [139]

  • -

    Protein–Ligand Interaction Profiler (PLIP) webserver [162]

 [163]
6 Test several anti-polymerase drugs against SARS-CoV-2 RdRp by using computational approaches
  • -

    Homology modeling

  • -

    Evaluating chemical properties, bonds, and angles of RdRp

  • -

    Molecular docking

  • -

    Toxicity validation and AdmetSAR profiling
  • -

    MODELLER [164]

  • -

    Molecular Operating Environment (MOE) software [133]

  • -

    AdmetSAR online tool [165]

 [166]
7 Investigate the effect of grazoprevir (antiviral drug against HCV) on SARS-CoV-2 by using in silico methods
  • -

    Protein selection and prediction

  • -

    Ligand selection and preparation

  • -

    Molecular docking

  • -

    Image generation and protein–ligand analysis

  • -

    Molecular dynamics simulation
  • -

    UCSF Chimera [167]

  • -

    SWISS-MODEL server [157]

  • -

    AutoDock 4.2 [168]

  • -

    Lig-Plot + [169]

  • -

    GROMACS [170], GROMOS 54A7 force field [171]

 [172]
8 Investigate the effect of probiotics (Plantaricin JLA-9, Plantaricin W, Plataricin D) on spike protein and the interaction of spike protein with human ACE2 receptor
  • -

    Protein modeling

  • -

    Generating model quality parameters

  • -

    Ligand preparation

  • -

    Ligand protein interaction and generation of images

  • -

    Molecular dynamics simulations; visualizing the graphs of Root Mean Square Deviation (RMSD)
  • -

    SWISS-MODEL server [157]

  • -

    Molecular Operating Environment (MOE) software [133]

  • -

    Discovery studio, UCSF Chimera package [167], and PLIP web server [162]

  • -

    GROMACS [170]

 [145]
9 Investigate the action of probiotic Lactobacillus plantarum Probio-88 against SARS-CoV-2 replication and immune regulation, with in silico study of metabolite Plantaricin E (PlnE) and Plantaricin F (PlnF) from Lactobacillus plantarum Probio-88
  • -

    Molecular docking
  • -

    SWISS-MODEL server [157]

  • -

    HADDOCK 2.4 [173]

  • -

    Visual Molecular Dynamics (VMD) [154]

 [147]