Compounds from P. murex have been identified, designed, optimised, and screened using docking to determine the most suitable natural compound that can inhibit V2R. Because its functionality is affected as a result of improper signalling, which affects the renal transporters as previously discussed, the V2R protein is a possible target protein in ADPKD.
2.1 Receptor structure identification
The sequence of the vasopressin V2 receptor isoform 1 (Homo sapiens) is retrieved from NCBI’s GenBank. The structure of the vasopressin V2 receptor isoform 1 (Homo sapiens) is predicted by Swiss-Model, an automated modelling server, by using the best template identified by the sequence alignment based on the expected value and scores. The atom coordinate file of the template structure is retrieved from PDB (Protein Data Bank) database. Predicted structure is then visualised, and energy is minimised using SwissPDBViewer (SPDBV), a structure visualization and analysis tool . Further, properties of the receptor are identified and validated by PROCHECK structure validation tool.
2.2 Binding/active site identification
In order to identify amino acids involved in receptor binding, a SCFBIO Tool (http://www.scfbio-iitd.res.in/) was used for the prediction of putative active site. The amino acids Val115, Lys116, Gln119, Met123 have been involved in the receptor binding and responsible for key functionality as per literature search [11, 12]. By targeting these amino acids, an aberrant signalling can be reduced or stopped. The active site/binding site dimensions were selected according to amino acids involved in receptor binding.
2.3 Compounds screening
The compound from P. murex was retrieved from the PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and the chemical structure was drawn by ChemSketch software (ACD/Labs Version 2020.2.1) . Further, open babel software (Version 3.1.1) has been used to convert molecular file formats of compounds . The library of ligand molecules was then subjected to virtual screening based on docking using PyRx software . PyRx classified the ligands according to their binding affinity, which represents the highest potential interaction with the receptor. The molecules with the lowest binding affinity (Kcal/mol) were chosen for further investigation of drug properties.
2.4 Drug properties identification
The pharmacological properties of the ligand molecules were identified by OSIRIS properties explorer [16,17,18]. The lipinski’s rule, molecular weight, H- bond acceptor, H-bond donor, clogp, druglikeness and drug score were analysed. The above-mentioned software was also used to investigate their mutagenic, tumorigenic, irritating, and reproductive effects. The compounds were then studied for molecular weight, clogp, topological polar surface area (TPSA), solubility, H-donor, H-acceptor, druglikeness, and total drug score. The software employed the logarithm of the partition coefficient between n-octanol and water, log(Coctanol/Cwater), to calculate compound hydrophilicity. Because high values imply poor absorption, substances with a clogp value of less than 5.0 have a high possibility of being well absorbed.
Drug absorption, including intestinal absorption, bioavailability, and blood–brain barrier penetration, has been identified by topological polar surface area (TPSA). It is a valuable measure for predicting drug transport characteristics. A compound’s water solubility has a considerable impact on its absorption and distribution characteristics. Low solubility is usually associated with poor absorption; therefore, the overall goal is to avoid poorly soluble compounds.
2.5 Docking verification and analysis
The shortlisted ligand molecule based on the drug properties and docking potential is again verified by AutoDock VINA. In addition, the discovery studio visualizer is used to visualise and analyse the shortlisted docked complexes . AutoDock VINA is a versatile molecular docking software that offers nine different docked ligand molecule modes with the receptor. The optimal mode with the lowest binding energy was chosen and studied for various bonding distances and interactions with the binding site residues.