*3.5. Molecular Dynamics (MD) Simulation*

Preliminary MD simulation for the energetically most favored quercetin 3-(6"-ferulylglucoside)-S-glycoprotein complex (determined by docking simulations) was conducted using YASARA Structure v. 20.12.24.W.64. Hydrogen (H)-bond optimization and pKa prediction for the chosen pH (7.4) were part of the experimental setup [36]. The addition of NaCl ions (0.9%, cell neutralization, and energy minimization provided the correct structure's geometry. The MD simulation was run for 12.50 ns with the AMBER14 force field. The setup used 298 K and one atmosphere for temperature and pressure values, respectively. The composition of the simulated system is given in Table S2.

#### *3.6. In Vitro SARS-CoV-2 Internalization Inhibition Assays*

To investigate the in vitro effects of *A. viridiflora* polyphenols on SARS-CoV-2 binding activity to ACE2 and NRP1 the MBS669459 screening kit (https://www.mybiosource.com/ covid-19-assay-kits/covid-19-coronavirus/669459 accessed on 29 June 2022) and RayBio COVID-19 Spike-NRP1 Binding assay kit (https://doc.raybiotech.com/pdf/Manual/CoV-NRP1S1\_2021.10.06.pdf accessed on 29 June 2022) were employed. Both assays were based on a colorimetric ELISA kit that measures the binding of RBD of the S-glycoprotein from SARS-CoV-2 (wild strain) to its human receptors ACE2 and NRP1, respectively. All tested samples were dissolved in phosphate buffer solution or DMSO the final concentration of which did not exceed 0.1%. Reagents preparation and assay procedure steps were conducted strictly following the provided protocols for the default configuration.

### **4. Conclusions**

The results of in vitro research, as well as in silico, showed that methanol extract of *A. viridiflora* and its components were capable of considerably inhibiting the internalization of SARS-CoV-2 through two of its currently most significant receptors. Ellagitannins more clearly blocked S-glycoprotein's interactions with ACE2, whilst flavonoids showed more affinity for interactions with the NRP1 receptor. Additionally, the structural changes to the S-glycoprotein brought on by mutations had a minor impact on the *A. viridiflora* constituens' activity. Lastly, the polyphenols found in the methanol extract of *A. viridiflora* offer intriguing starting points for future in vitro and in vivo anti-SARS-CoV-2 research, particularly considering their potential synergistic activity.

**Supplementary Materials:** The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/molecules27165174/s1. Figure S1: *A. viridiflora* methanol extract mass spectrum; Figure S2: *A. viridiflora* methanol extract base peak chromatogram; Figure S3: Graphical presentation of binding pockets with constituent amino acid residues (ball and stick display style) for protein targets used in docking simulations (a) S-glycoprotein (PDB:7BZ5) with binding pocket residues marked red; (b) Neuropilin-1 (PDB:2QQI) with binding pocket residues marked blue; Figure S4: A ray-traced picture of the simulated system. The simulation cell boundary is set to periodic; Figure S5: Total potential energy of the system [vertical axis] as a function of simulation time [horizontal axis]; Figure S6: Radius of gyration of the solute [vertical axis] as a function of simulation time [horizontal axis]; Figure S7: Ligand movement root mean square deviation (RMSD) after superposing on the receptor [vertical axis] as a function of simulation time [horizontal axis]; Table S1: Binding pocket residues list for protein targets used in docking simulations; Table S2: Composition of the simulated system.

**Author Contributions:** Conceptualization, design, acquisition of data, analysis and interpretation of data, writing—original draft preparation R.S. and R.Š.; acquisition of data, analysis and interpretation of data J.R.S., T.K.-V., L.S., B.L. and M.T. All authors have participated in reviewing and editing the article critically for important intellectual content. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by the Ministry of Education, Science and Technological Development, Republic of Serbia through Grant Agreement with University of Belgrade-Faculty of Pharmacy No: 451-03-9/2021-14/200161.

**Institutional Review Board Statement:** Not applicable.

**Informed Consent Statement:** Not applicable.

**Data Availability Statement:** All data are available upon reasonable request.

**Conflicts of Interest:** The authors declare no conflict of interest.
