Table 2.
General summary of research topics and results on hesperidin as potential compound against SARS-CoV-2 in silico studies.
| References | Computational Techniques | Biological Targets of SARS-CoV-2 |
Effectiveness Outcomes |
|---|---|---|---|
| [15] | 1. Molecular docking 2. Molecular dynamic simulations |
Mpro, S protein, RdRp, nsp13 | 1. Strong binding affinity with viral proteins |
| [48] | 1. Molecular docking 2. Quantum chemical density functional theory calculations |
Mpro, S protein | 1. Binding affinity 2. Inhibitory effects on viral replication 3. Comparative analyses with standard antiviral drugs |
| [49] | 1. Molecular docking | S protein, hACE2 | 1. Interactions with key residues of the spike protein and ACE2 receptor |
| [50] | 1. Molecular docking 2. Molecular dynamics simulations |
S protein, hACE2 | 1. Non-competitive modulator that destabilizes the interaction between the spike protein and the ACE2 receptor |
| [51] | 1. Molecular docking 2. Virtual screening |
Mpro, hACE2, PLpro, HR1, RBD | 1. Affinity to bind 2. Interact with key viral proteins 3. Interfere with virus-host interactions, inhibit viral replication |
| [52] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, S protein, RdRp, TMPRSS2, hACE2 | 1. Inhibitory effect on virus replication, entry and infectivity 2. Potential to modulate host immune response against SARS-CoV-2 |
| [53] | 1. Molecular docking 2. Molecular dynamics simulations |
S protein, RdRp | 1. Binding affinity, stability and potential inhibitory effect on viral proteins |
| [54] | 1. Gaussian09 software for electronic calculations 2. Density functional theory 3. Conceptual density functional theory for antioxidant properties |
Mpro, S protein, RdRp | 1. Evaluation of the ability to interact with viral components 2. Potential inhibition of viral replication |
| [55] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro | 1. Binding affinity to viral proteins, particularly Mpro 2. Potential inhibitor of viral replication and maturation |
| [56] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro | 1. Binding energy, binding sites, key interactions with viral proteins |
| [57] | 1. Molecular docking 2. Molecular dynamics simulations 3. Pharmacokinetic studies |
S protein | 1. Inhibiting viral proteins or disrupting viral-host interactions, as evidenced by favorable binding affinities, pharmacokinetic properties 2. Potential inhibitory effects on viral entry or replication. |
| [58] | 1. Molecular docking 2. Molecular dynamics simulations 3. MM-GBSA analysis |
Mpro, S protein, RdRp, N protein, E protein | 1. Binding energy values and key residue interactions 2. Drug-likeness assessments 3. ADMET properties |
| [59] | 1. Molecular docking 2. Molecular dynamics simulations 3. Virtual screening 4. Quantitative structure-activity relationship analysis |
S protein, RBD, hACE2 | 1. Key interactions identification 2. Binding energies 3. Inhibition constants and mechanism of action |
| [60] | 1. Molecular docking 2. Structure-based virtual screening |
RBD, hACE2 | 1. Inhibit the SARS-CoV-2-ACE2 interaction, suggesting a possible role in preventing viral cellular entry |
| [61] | 1. Molecular docking 2. Molecular dynamics simulations 3. Free energy calculations 4. Target prediction algorithms |
Mpro, RdRp | 1. Binding affinity 2. Stability of protein-ligand complexes 3. Inhibitory activity against viral proteins |
| [62] | 1. Molecular docking 2. Blind docking analyses |
Mpro | 1. Estimated free energy of binding for the main protease |
| [63] | 1. Molecular docking 2. Molecular dynamics simulations 3. Virtual screening 4. Deep learning tools for drug-target interaction predictions |
Mpro | 1. Potential inhibitor of SARS-CoV-2. Targeting key viral proteins |
| [64] | 1. Molecular docking 2. Molecular dynamics simulations |
S protein | 1. Binding affinity, stability, and specific interactions with viral |
| [65] | 1. Molecular docking 2. Molecular dynamics simulations 3. Binding free energy calculations |
Mpro, S protein | 1. Inhibiting viral replication 2. Blocking viral entry into host cells 3. Modulating the host immune response |
| [66] | 1. Molecular docking 2. Machine learning approaches |
Mpro, S protein | 1. Potential inhibitor of Mpro 2. Binding interactions and potential antiviral activity |
| [67] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, S protein, hACE2 | 1. Binding affinity scores 2. Interaction energies 3. Key residues involved in hesperidin-protein interactions 4. Constant inhibition or IC50 values for quantifying the potency of hesperidin as an antiviral agent |
| [68] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro | 1. Promising binding energies 2. Interactions at Mpro active site |
| [69] | 1. Molecular docking 2. Binding affinity tests, including biolayer interferometry assay and isothermal titration calorimetry assay |
Mpro, hACE2, S protein, RBD | 1. Binding affinity with ACE2, M, S, RBD proteins 2. Impact on immune, inflammation, virus infection, IC50 values (51.5 μM and 5.5 mM) |
| [70] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, S protein, hACE2 | 1. Binding energies 2. Interaction patterns 3. Key amino acid residues 4. Evaluate stability and dynamics of complexes |
| [71] | 1. Molecular docking 2. Molecular dynamics simulations 3. Pharmacophore modeling |
Mpro, S protein, RdRp, PLpro, nsp13 | 1. Evaluate binding affinity, stability, potential to inhibit viral replication |
| [72] | 1. Molecular docking 2. Molecular dynamics simulations 3. SwissADME and ProTox-II for drug-likeness and toxicity assessment |
Mpro, TMPRSS2, PLpro | 1. Strong complex formation 2. Stable interactions with viral proteins |
| [73] | 1. Molecular docking 2. Molecular dynamics simulations 3. Molecular modeling techniques |
nsp13, ExoN, Guanine-N7 methyltransferase | 1. Interactions with critical residues of target proteins |
| [74] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, RdRp | 1. Binding affinity 2. Stability in forming complexes with viral enzymes 3. Potential multi-target inhibitory activity |
| [75] | 1. Molecular docking 2. Molecular dynamics simulations 3. Virtual screening |
nsp16,2′-O-methyltransferase | 1. Promising interactions with key residues of the nsp16 protein |
| [76] | 1. Molecular docking 2. Molecular dynamics simulations 3. ADMET for drug properties |
Mpro, RdRp | 1. Superior binding affinities with Mpro, RdRp compared to standard drugs 2. Strong interactions with catalytic residues |
| [77] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, S protein, hACE2 | 1. Inhibitory effects on viral proteins 2. Disruption of viral entry mechanisms 3. High binding affinities to key viral targets |
| [78] | 1. Molecular docking 2. Molecular dynamics simulations |
Mpro, allosteric site | 1. Identified potent allosteric inhibitors |
Mpro—SARS-CoV-2 main proteinase; S protein—SARS-CoV-2 spike glycoprotein; hACE2—human angiotensin-converting enzyme 2 receptor; RdRp—RNA-dependent RNA polymerase; nsp13—non-structural protein 13 (helicase); PLpro—papain-like protease; HR1—heptad repeat 1 domain; RBD—receptor binding domain; TMPRSS2—transmembrane serine protease 2; N Protein—ucleocapsid protein; E protein—envelope protein; ExoN—exoribonuclease.