Chemsketch

The two-dimensional (2D) structure of sinigrin (2-propenylglucosinlate) was retrieved from the NCBI PubChem database with the following accession number CID: 5464493. This molecule was drawn using ChemSketch (Advanced Chemistry Development, Inc. Toronto, ON, Canada), saved in a 2D (.mol) format, and then converted into a 3D (.pdb) format by importing into Discovery Studio 3.5 visualizer (DS 3.5) (DS, Accelrys, Inc. SanDiego, CA, USA). This molecule was optimized using the Conjugate Gradients method [46 (link)] followed by Steepest Descent in 200 steps using the PyRx program [47 (link)]. Universal Force Field (UFF) was used for minimization of the sinigrin molecule [48 (link)]. Molecular docking analysis was performed using AutoDock Vina [49 (link)]. Active site residues were carefully assigned to the binding pocket of the MYR protein, and docking steps were followed from previous studies [50 (link)]. The best docking orientation was identified from binding affinity score and hydrogen bond interaction to the active site based on visual inspection. The 2D graphical visualization of MYR and sinigrin interaction was generated by DS 3.5. The X-Score program [51 (link)] was used to calculate binding affinity scores of sinigrin and non-bonded interactions.

The average values from at least three or more independent experiments are shown ± SD. The explicit explanation of the statistical analyses performed using the GraphPad Prism Software version 6 is included in each figure legend text together with p values. Western blots were repeated at least three times. Chemical structures were created using ChemSketch, freeware version, Advanced Chemistry Development, Inc. (ACD/Labs), Toronto, ON, Canada, www.acdlabs.com. The scheme in Fig. 6 was created with BioRender.com.

The protein crystal structure of the receptor-binding domain complexed with its receptor human ACE2 was obtained from the RCSB protein databank (rcsb.org, PDB: 6VW1)^{17 (link),40 (link)}. The spike protein was prepared by the Protein Preparation Wizard in Schrödinger suite⁴¹ . The missing side chains were fixed by Prime⁴² . The APS sensor molecule was prepared by Chemsketch (Advanced Chemistry Development, Inc.). The interaction information was extracted and refined by the Enhanced Ligand Exploration and Interaction Recognition Algorithm (ELIXIR-A) platform^{43 (link)}. Molecular docking was performed using the software Autodock vina with the default protocol^{44 (link)}. The protein–ligand interactions were analyzed in Maestro⁴⁵ .

The structure of CXCR3 was generated by homology modeling using the crystal structure of the CXCR4 chemokine receptor in a complex with small-molecule antagonist IT1t resolved at 2.5 Å (PDB file 3ODU) as a template.[34 (link)] The CXCR3 sequence was aligned with the CXCR4 sequence in PDB file 3ODU using default parameters of Maestro graphical user interface of Schrodinger Suite (Schrodinger LLC, NY). The homology model was generated by the ‘Prime’ program of the Schrodinger Suite. During homology modeling, compound IT1t was removed. The final structure was subjected to restricted minimization (1,000 iterations) by ‘Impact’ module of Schrödinger Suite with OPLS_2005 force field. The resultant structure was used to identify suitable ligand binding pockets using (i) SiteMap (Schrödinger Suite, NY), and (ii) SiteID (Certara, Tripos Associates, St. Louis, MO) programs. The spatial structure of 1 was generated using the ChemSketch program (Advanced Chemistry Development, Toronto, Canada). The structure was subject to ‘LigPrep’ utility of Schrodinger Suite to generate the molecules suitable for the docking. The docking of 1 was conducted with ‘Glide’ (Schrodinger Suite) with XP (extra precision) option. The docked pose with the greatest docking score was selected to generate the figure using PyMol (Schrodinger LLC., NY).

The X-ray crystal structure of native HIV-1 capsid protein bound to PF74 (PDB entry 4XFZ) (Gres et al., 2015 (link)) was used to dock GS-CA1 and Coumermycin A1 (C-A1). Initial structures of GS-CA1 and C-A1 were generated with ChemSketch (Advanced Chemistry Development, Inc., Toronto, Ontario, Canada). These structures were subsequently minimized using MacroModel followed by LigPrep (Schrödinger Inc. NY). The PrepWizard (Schrödinger Inc. NY), which adds hydrogens, assigns bond orders, creates heteroatom states, and samples conformations of water molecules, was used to prepare CA-hexamer for docking of GS-CA1 and C-A1.