112
5. Gaussian 09: [17] A program for electronic structure calculations (license fee required). Gaussian was used to perform IRB
optimization and RESP charge derivation for IRB and
2-HP-β-CD (https://gaussian.com/).
6. UCSF CHIMERA 1.12: [18] A program for visualization and
analysis of biomolecules (free of charge). CHIMERA was used
for structure visualization, and figure generation (https://
www.cgl.ucsf.edu/chimera/).
3 Methods
Obtain the crystal structures of IRB and 2-HP-β-CD from the
CSD and PubChem, respectively. The reference codes correspond
to CCDC: 130127 for IRB and PubChem CID: 14049689 for
2-HP-β-CD. Save the structures in PDB formats (IRB.pdb and
2-HP-β-CD.pdb).
Molecular docking of IRB into 2-HP-β-CD: IRB can be included
into the cavity of 2-HP-β-CD in two different orientations. The
first orientation considers the tetrazole moiety of IRB near the HP
end of 2-HP-β-CD, while the opposite orientation associates the
butyl alkyl chain of IRB with the HP group (Fig. 2). The optimal
placement of IRB in its two orientations into 2-HP-β-CD and the
binding strength was predicted with ArgusLab. It is noted that any
other suitable docking software can also be applied. For the sake of
simplicity, hereafter we may occasionally refer only to one
orientation.
Open the main panel in ArgusLab and perform the following
steps:
1. Open molecule (browse and upload ligand).
2. The name of selected ligand (IRB.pdb) appears on the left-side
panel. Click on the cross to expand; on the extended menu click
Residues and then Misc. Next, select the molecule that appears
(i.e., 1 MOL) and right-click. On the new menu, select Make a
Ligand Group from this Residue.
3. Repeat the procedure for the receptor: open molecule in the
main panel and browse to upload 2-HP-β-CD.pdb.
4. Repeat step 2 and after clicking Misc, select all 2-HP-β-CD
subunits that appear. On the new menu, select Make a Group
from this Residue. Next select Binding Site.
5. In the main window, press Calculation → Dock a Ligand. A
new menu appears with a list of docking parameters. Most of
the default selections will suffice for a rough estimation. The
user should carefully experiment and choose among various
3.1 Molecular
Modeling
3.1.1 Structure Retrieval
3.1.2 Molecular Docking
Calculations
Georgios Leonis et al.
5. Gaussian 09: [17] A program for electronic structure calculations (license fee required). Gaussian was used to perform IRB
optimization and RESP charge derivation for IRB and
2-HP-β-CD (https://gaussian.com/).
6. UCSF CHIMERA 1.12: [18] A program for visualization and
analysis of biomolecules (free of charge). CHIMERA was used
for structure visualization, and figure generation (https://
www.cgl.ucsf.edu/chimera/).
3 Methods
Obtain the crystal structures of IRB and 2-HP-β-CD from the
CSD and PubChem, respectively. The reference codes correspond
to CCDC: 130127 for IRB and PubChem CID: 14049689 for
2-HP-β-CD. Save the structures in PDB formats (IRB.pdb and
2-HP-β-CD.pdb).
Molecular docking of IRB into 2-HP-β-CD: IRB can be included
into the cavity of 2-HP-β-CD in two different orientations. The
first orientation considers the tetrazole moiety of IRB near the HP
end of 2-HP-β-CD, while the opposite orientation associates the
butyl alkyl chain of IRB with the HP group (Fig. 2). The optimal
placement of IRB in its two orientations into 2-HP-β-CD and the
binding strength was predicted with ArgusLab. It is noted that any
other suitable docking software can also be applied. For the sake of
simplicity, hereafter we may occasionally refer only to one
orientation.
Open the main panel in ArgusLab and perform the following
steps:
1. Open molecule (browse and upload ligand).
2. The name of selected ligand (IRB.pdb) appears on the left-side
panel. Click on the cross to expand; on the extended menu click
Residues and then Misc. Next, select the molecule that appears
(i.e., 1 MOL) and right-click. On the new menu, select Make a
Ligand Group from this Residue.
3. Repeat the procedure for the receptor: open molecule in the
main panel and browse to upload 2-HP-β-CD.pdb.
4. Repeat step 2 and after clicking Misc, select all 2-HP-β-CD
subunits that appear. On the new menu, select Make a Group
from this Residue. Next select Binding Site.
5. In the main window, press Calculation → Dock a Ligand. A
new menu appears with a list of docking parameters. Most of
the default selections will suffice for a rough estimation. The
user should carefully experiment and choose among various
3.1 Molecular
Modeling
3.1.1 Structure Retrieval
3.1.2 Molecular Docking
Calculations
Georgios Leonis et al.