Molecular docking based virtual screening of carbonic anhydrase IX with coumarin (a cinnamon compound) derived ligands

It is of interest to design carbonic anhydrase IX (CAIX) inhibitors with improved features using molecular docking based virtual high through put screening of ligands. Coumarin (a cinnamon compound with pharmacological activity) is known as a potent phytal compound blocking tumor growth. Hence, a series of 17 coumarin derivatives were designed using the CHEMSKETCH software for docking analysis with CAIX. The catalytic site analysis of CAIX for binding with ligand molecules was completed using the SCHRODINGER package (2009). Thus, 17 ligands with optimal binding features with CAIX were selected following the calculation of ADME/T properties. We report ligands #41, #42, #19 and #15 showed good docking score, glide energy and hydrogen bond interactions without vdW clash. We further show that N-(3,4,5-trimethoxy-phenylcarbamoylmethyl) designated as compound #41 have the highest binding energy (-61.58) with optimal interactions with the catalytic residues (THR 199, PRO 201, HIS 119, HIS 94) of CAIX.


Methodology: Target
The protein molecule chosen for the docking studies is carbonic anhydrase-IX. The target structure data is downloaded from the Protein Data Bank (PDB; http://www.rcsb.org/ pdb/home/home.do). The crystal structure of the protein taken for the docking studies (PDB code: 3IAI) with resolution of 2.2 Ǻ is shown in Figure 2. Water molecules are removed from the structure and hydrogen atom was added for further process.

Ligand selection and preparation:
A total of 17 derivatives of coumarin were selected for molecular screening, based on comprehensive literature survey for natural compounds with anti-tumor activity. Ligand structures are drawn using the CHEMSKETCH software ( Table 1). This is used for high throughput virtual screening of a new potential drug for CAIX. Minimization by geometric optimization using OPLS_2005 is carried out for ligands to have correct bond orders and bond angles.

Grid generation:
Residues of each active site in CAIX were scaled with a van der Waal's radii of 1.0 Å havng partial atomic charge less than 0.25 Å. The gird was generated around active sites using QSITEFINDER and SITEMAP enclosed by a box at the center of selected residues.
Docking studies: CAIX docking with coumarin was completed using the GLIDE docking tool. Glide score contains a number of parameters such as vdW, Hydrogen bond (H bond), columbic (Coul), hydrophobic (Lipo), polar interactions in the binding site (site), metal binding term (metal) and penalty for buried polar group (Burry P) and freezing rotatable bonds (RotB).

ADME/T properties:
Absorption, Distribution, Metabolism, Excretion and Toxicity (ADME/T) properties of the docked molecules were predicted using QIKPROP tool in Schrodinger. This predicts the properties such as logBB, octanol/water partition, overall CNS activity and log IC50 values.

Results:
The crystal structure of CAIX (PDB ID: 3IAI), with a resolution of 2.20 Å (Figure 2) and coumarin derivatives shown in Table 1 were used for the docking studies. The structures of ligands were drawn using the CHEMSKETCH software. Energy minimization was done by using OPLS_AA force field. The protein structure and the ligands of coumarin derivatives are subjected to High Throughput Virtual Screening (HTVS) using yje GLIDE HTVS 5 module. The possible conformations of the best ligands and native ligand along with their docking score and Glide energy is given in Table 2. HTVS 5 selected compounds were subjected to Induced Fit Docking (IFD). IFD allows the receptor to alter its binding sites to mimic the shape and binding mode of the ligand. IFD were carried out between the target protein and screened ligands using GLIDE followed by PYMOL visualization. Table 3 and Figure 3 shows the possible conformations of best ligands comparing the native ligand along with their docking score and GLIDE energy. The ADME/T properties of these compounds were further analyzed using the QIKPROP tool of Schrodinger software. This is followed by PASS prediction on the basis of activity proportional to structure.

Discussion:
Carbonic anhydrase IX has a very high catalytic activity for the hydration of carbon dioxide to bicarbonate and protons. This is used as a marker of tumor hypoxia and as a prognostic factor for many human cancers. Coumarins constitute totally a new class of inhibitors of the zinc enzyme carbonic anhydrase, which bind at the entrance of the active site. The PDB structure (PDB ID: 3IAI) and 747 ©Biomedical Informatics (2019) the coumarin derivatives were used for docking analysis. The ligands did not have correct bond orders and bond angles. Hence, the missing hydrogen atoms and unfilled valence atoms were corrected using the OPLS_2005 force field. The active sites are predicted using Q-SITE FINDER and SITEMAP [30,31] for further screening and docking analysis. GLIDE module from the Schrodinger package is used for docking analysis. All the ligands were minimized and subjected to High Throughput Virtual Screening ( Table 2). Parameter such as G-Score, Glide Energy, Hbonds and Good Van-der-walls interactions were estimated. The more negative value of GLIDE score indicates that good binding affinity of ligand with receptor.

Conclusion:
We show that N-(3,4,5-trimethoxy-phenylcarbamoylmethyl) designated as compound #41 have the highest binding energy (-61.58) with optimal interactions with the catalytic residues (THR 199, PRO 201, HIS 119, HIS 94) of CAIX for further consideration and evaluation using in vitro and in vivo models.