Molecular docking is used to determine the binding characteristics between a ligand and a protein [8]. A large number of tools are available for this purpose but in this study only a few of those was used. Several websites and softwares are included in this process. These all are used step by step and the list is given bellow:
PubChem (https://pubchem.ncbi.nlm.nih.gov/), Protox (http://tox.charite.de/protox_II/), Swiss target prediction (http://www.swisstargetprediction.ch/), RCSB Protein Data Bank (https://www.rcsb.org/), Flare, PyMol, Swiss PDB, PyRx.
Here the combination ‘Olmesartan medoxomil & Hydrochlorothiazide’ had been considered. Two drugs could not be taken at a time, so the same procedures were separately followed for both drugs one by one. First, the drug ‘Olmesartan medoxomil’ had been considered. From PubChem the structure of Olmesartan medoxomil had been searched and the ‘Canonical SMILES’ had been copied [9, 10]. That is:
CCCC1=NC(=C(N1CC2=CC=C(C=C2)C3=CC=CC=C3C4=NNN=N4)C(=O)OCC5=C(OC(=O)O5)C)C(C)(C)O
The SMILES had been pasted in Protox [11]. From protox, informations about probable toxicities that might be showed by the drug had been obtained. It had been seen that the drug has active immunotoxicity (probability 0.96) [11]. After that Swiss Target Prediction had been used [12]. By pasting that canonical SMILES in the search option, the names of the proteins with which the drug might interact and the probabilities of those bindings had been observed [12]. A long list containing about 68 proteins had been obtained. Some of these proteins are responsible for the drug’s desired effect. By binding with these proteins ‘Olmesartan medoxomil’ shows its hypertension lowering effect. But simultaneously the drug also binds with some other proteins in the system, that may not show any beneficial effect that enhances its’ quality and acceptability as an antihypertensive drug. Among these proteins two proteins had been considered for docking purpose using Autodock Vina [13]. Those two proteins are:
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I.
Tyrosine-protein kinase JAK2
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II.
Angiotensin II receptor
From Protox it had been known that the drug might show immunotoxicity. After searching about the proteins with which the drug binds and might cause immunotoxicity had been identified then cleaned and saved properly. Those are:
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1.
Caspase-8
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2.
COX-2
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3.
ADAM-17
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4.
Complement Factor-D
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5.
Endothelin receptor ET-B
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6.
Caspase-3
The 3D structures of these proteins had been downloaded from Protein Data Bank with resolution of 2–2.5 Å [14]. But those raw structures cannot be used for docking purpose. These structures not only consist of the desired protein portions but also some unnecessary spaces, amino acids, fatty acids, water molecules, other side molecules. So before using these for docking these unnecessary portions should be cleaned. This can be done by using PyMol software [15]. Sometimes while downloading any protein structure from the Protein Data Bank, the exact protein structure is not found. Rather the protein may be found in a complex form with other ligand that is not of our interest or protein–protein complex may also be found. In those cases, the software named Flare is used to edit the protein–ligand complex or protein–protein complex. The unnecessary ligand portion or protein chain is cut down from the desired protein portion. After doing all these processes a cleaned form of the desired protein is saved for further use. The cleaned protein structures had been opened in swiss PDB and energy minimization had been done so that the docking can be done properly [16]. Energy minimization is done to reduce the potential energy of the protein and ligand. The bond lengths and bond strengths inside the protein makes the protein and ligand unstable. So energy minimization is done prior to docking to get the optimal binding of the desired ligand with the desired protein [17]. As docking cannot be done in both cases when the protein’s or ligand’s size is either too big or too small. In maximum cases ligands are of small size, that’s why energy minimization is not done in case of ligands. So in most of the cases energy minimization is done only for the proteins to make them stable [17]. These energy-minimized proteins had been saved for the next docking purpose. After preparing all target proteins and ligand, pyRx software had been used for the docking purpose [18]. Each protein had been docked with the ligand (Olmesartan medoxomil) and the result had been observed and interpreted properly (Figs. 1, 2, 3, 4, 5, 6).
All the procedures that had been followed for Olmesartan medoxomil, once again those had been used step by step for Hydrochlorothiazide to determine the target proteins, by binding with which of them Hydrochlorothiazide shows intended effect and with which it shows toxicity. But no toxicity profile was found in case of Hydrochlorothiazide [11].
