MOLECULAR DOCKING VIRTUAL SCREENING, DRUG-LIKENESS AND PHARMACOKINETICS (ADMET) PROPERTIES PREDICTION OF SOME ENDOMETRIAL CANCER AGENTS

Endometrial or uterine cancer is a malignancy arising from the endometrium of the uterus. Women have a 1 in 40 life-time risk of being diagnosed with endometrial cancer, the fourth most common malig¬nancy among women. Endometrial cancer is the most common gynecological malignancy in the developed world. The binding mode of some endometrial cancer agents in the active site of human estrogen receptor (PDB1*1P) (receptor) was studied via molecular docking. Molecule 6 was identified to have the highest binding energy of -10.1 kcal/mol among other selected compounds which might be as a result of hydrogen bond interactions formed with ASP480 amino acid residues and hydrophobic/other interactions formed with LEU508, LEU479 and ILE451 amino acid residues in the active site of the receptor. The drug-likeness properties of these selected endometrial cancer agents were predicted following the Lipinski’s rule of five and were found to be orally active and bioavailable as they obeyed the used filtering criterion. Based on the pharmacokinetic properties predicted, they were seen to have good ADMET properties. This research proposed a way for designing potent endometrial cancer agents against their target enzyme (human estrogen receptor).


INTRODUCTION
Cancer is a chronic abnormal cell disorder or a lethal disease demonstrates by immortality and unrestricted cell division. Cancer cells may be invasive, aggressive and metastatic and generally spread into various organs in the body (Jemal et al., 2011). Endometrial or uterine cancer is a malignancy arising from the endometrium of the uterus. Women have 1 in 40 lifetime risk of being diagnosed with endometrial cancer, the fourth most common malig¬nancy among women (Barr et al., 2016). Uterine cancer is the most common gynecologic malignancy in the United State. Stage I malignancies comprises the majority of endometrial cancers. Postmenopausal bleeding is the most common presentation (Boggess et al., 2008). Endometrial cancer is the most common gynecological malignancy in the developed world. The majority of cases can be divided into two broad categories based on clinicpathological and molecular characteristics; Type I oestrogendependent with endometrioid morphology and Type II nonestrogen-dependent with serous papillary or clear cell morphology (Llauradó et al., 2012). The concept of computational chemistry like computer-aided drug design (CADD) might save the time of discovering or designing new compounds with better potency, and also reduce the cost of synthesis. Molecular docking virtual simulation is very important when carrying out a structurebased drug design (SBDD) which predicts the binding affinities an orientation when two molecules bind with each other to form a stable complex (Ibrahim et al., 2021). Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding conformation of the small molecules to the appropriate target binding site (Ferreira et al., 2015). Characterization of the binding behavior plays an important role in the rational design of drugs as well as elucidating the fundamental biochemical processes. Molecular docking in the pharmaceutical industry is powerful in silico approach for discovering of novel therapies for unmet medical needs predicting drug-target interactions, it provides binding affinity between drugs and target at the atomic level and elucidates the fundamental pharmacological properties of a specific drug (Shadrack et al., 2018). Drug-likeness properties give the conditions or criteria for a drug potency of a particular chemical compound. include the use of Lipinski's rule of five to predict the drug-likeness of the selected drugs, which states that if any chemical violates more than two of these criteria (Molecular weight ≤ 500g/mol, Number of hydrogen bond donor ≤ 5, Number of hydrogen bond acceptors ≤ 10, calculated Log P ≤ 5 and the molecule are said to be impermeable or badly absorbed (Li et al., 2019;Lipinski, 2004). The ADMET properties also known as pharmacokinetics properties describe the fate of a small molecule (drug/ligand) in the body of a living organism. The acronym stands for absorption, distribution, metabolism excretion and toxicity (ADMET) (Olasupo et al., 2020). The aim of this study is to virtually screen and predict the pharmacokinetics properties of some endometrial cancer inhibitors.

MATERIAL AND METHODS Software and computational environment
A HP655-PC computer system with the following specification: AMD E1-1200 APU with Radeon at 1.40GHz, 4GB of RAM was utilized to explore the nature of interactions between the active site of estrogen and the compounds under investigation (ligands) with the help of Pyrex virtual screening software, Chimera and Discovery studio.

Data collection
Twenty-two (22) sets of endometrial cancer agents were gotten from the literature and used in this work.

Structure generation, stable geometry calculations and ligand preparation
In this work, the 2D structures of the dataset were drawn using Chemdraw 12.0 software. After generation of the 2D structure of the studied molecules, the 2D structures were automatically converted to 3D by the Spartan 14 software before energy minimization. Energy minimization was carried out to reduce constraints in the structures before finding the most stable geometry of the studied molecules. The most stable geometry of the studied molecules was ascertained using density functional theory (DFT) at B3LYP/6-311G* level of theory. Ligands were prepared before the docking analysis from the optimized structure of the drugs and saved in pdb file format using Spartan 14 (Ibrahim et al., 2020a).

Protein retrieval and preparation
The 3D structure of the receptor was retrieved from the RCSB pdb database. The enzyme was prepared with the help of a discovery studio visualizer for the docking analysis. In the course of its preparation, polar hydrogen was added. Water molecule and co-ligands were eliminated from the crystals structure and saved in pdb file format (Abdullahi et al., 2020).

Docking based virtual screening analysis
The docking of the ligands to the binding pose of the enzyme was achieved with the help of Autodock vina of Pyrex virtual screening software. After a successful docking procedure, since Pyrex was used there is a need to re-couple the docked ligand and the receptor for further investigation (Ibrahim et al., 2020b). UCSF Chimera software was used for the re-coupling of the docked ligand and the receptor. Discovery studio was used to achieve the visualization of recoupled complexes in order to view the nature of the interaction between the ligand and the receptor (Ibrahim et al., 2019).

RESULTS AND DISCUSSION Molecular docking
The nature of the interactions between some endometrial cancer agents and the active site of human estrogen receptor alpha (PDB ID 1*1P) was studied using molecular docking. Table 1 shows the binding affinities and mode of interaction of the studied molecules. The binding affinities of the studied molecules range from -3.3 Kcal/mol to -10.1 Kcal/mol, respectively. From the result of the docking virtual screening (Table 1), molecule 6 was identified to have the highest binding affinity of -10.1 Kcal/mol among the other selected compounds followed by molecule 19 with the binding affinity of -9.0 Kcal/mol, molecule 17 with a binding affinity of -8.8 Kcal/mol, molecule 2 with a binding affinity of -8.1 Kcal/mol and molecule 4 having the lowest binding affinity of -3.3 Kcal/mol among the studied molecules.  Table 1, molecule 6 the most potent identified mol among other selected compounds with a binging affinity -10.1 Kcal/mol formed a conventional hydrogen bond with ASP480 and carbon-hydrogen bond with the following amino acid residues ASN455, HIS476, THR483, LEU504 and LEU509, respectively which might be primarily responsible for its high binding affinity. Not only the mentioned ones but also hydrophobic and other interactions with LEU508, LEU479 and ILE451 amino acid residues were observed. The 2D structure of molecule 6 in complex with the human estrogen receptor alpha is shown in Figure 1. Next among the molecules identified with higher binding affinities was molecule 19 (-9.0 kcal/mol) where it interacted with the active site of the human estrogen receptor alpha through a conventional hydrogen bond with LEU346 amino acid residue. Besides this, it also interacted with the active site of the human estrogen receptor alpha through carbon-hydrogen bonds with ARG548, ASP545 and ARG363 amino acid residues, respectively. Not only had that, but it also formed hydrophobic and other interactions with ILE326, LEU403, LYS531, ASN532, ASP351, PRO535 and VAL533 amino acid residues, respectively. The 2D structure of molecule 19 in complex with the human estrogen receptor alpha is shown in Figure 2. The third molecule identified with higher binding affinity was molecule 17 (-8.8 Kcal/mol). The conventional hydrogen bond between the molecule and active site of the human estrogen receptor alpha with GLU353 and ARG394 amino acid residues were observed. HIS398, SER395, MET396, PRO325, PRO406 and ARG394 amino acid residues in the active site of the human estrogen receptor-alpha were seen to have formed a carbon-hydrogen bond with molecule 17, respectively. Hydrophobic and other interactions between the molecule and LEU384, LEU525, ILE424 and THR347 amino acid residues were also observed. The 2D structure of molecule 17 in complex with the human estrogen receptor alpha is shown in Figure  3. The one that comes after molecule 17 among the identified ones with higher binding affinities was molecule 2 (-8.1 Kcal/mol). It was seen to form a conventional hydrogen bond with LEU409 and GLN414 amino acid residues and a carbon-hydrogen bond with LEU408, LEU410, TYR331, ASN407, PRO333 and LYS408 amino acid residues, respectively. Apart from the conventional and carbon-hydrogen bonds, it formed hydrophobic and other interactions in the active site of the human estrogen receptor alpha with PHE337, PHE425, CYS530, ILE424 and PHE404 amino acid residues, respectively. The 2D structure of molecule 2 in complex with the human estrogen receptor alpha is shown in Figure 4.

Drug-likeness properties
The drug-likeness properties of all the endometrial cancer agents were predicted to confirm the viability of the drugs employing SWISSADME online web tools. The drug-likeness properties of the reported compounds are presented in Table 2. From the Table, none among the identified compounds with higher binding affinities was found to violate any of the condition/ criteria (Molecular weight ≤ 500, Number of hydrogen bond donors ≤ 5, Number of hydrogen bond acceptors ≤ 10, and Calculated Log p ≤ 5) set by the Lipinski's rule of five. This confirms that the identified compounds are orally active and bioavailable. The plot of WLOGP against TPSA (Boiled-egg plot) to predict gastrointestinal absorption and brain penetration of the selected molecules was shown in Figure 5. It can be seen from the plot that only a few of the molecules possess the BBB permeability properties. Almost all of the studied compounds are within the GI absorption region except three (3) compounds.

ADMET properties
The pharmacokinetic (ADMET) properties of all the endometrial cancer agents were predicted employing pkCSM online web tools. The ADMET properties of the reported compounds are shown in Table 3. All the reported compounds have absorbance values between 36.5 to 100% as the values passed the minimum recommended values of 30% which indicates good human intestinal absorption. The minimum recommended values for the blood-brain barrier (BBB) and central nervous system permeability is > 0.3 to < -1 Log BB and > -2 to < -3 Log PS respectively. As for these compounds, Log BB is between -0.122 to 1.038 for all which implies that the compounds are better distributed to the brain except for those that are not within the accepted values. Log PS for all is between -0.696 to -3.895 which are considered to penetrate the central nervous system except for those that are not within the accepted values. The enzymatic metabolism of drugs shows the biotransformation of a drug in the body. The most important among the CYP families is 3A4 which is the reported compounds were found to be substrate and inhibitors of it including the identified potent compounds. The reported compounds showed a high value of total clearance but within the accepted limit of a drug molecule in the body. Furthermore, all the reported compounds were found to be non-toxic except a few. The overall ADMET properties of these compounds most especially the identified compounds indicate their good pharmacokinetic profiles (Table 3).

CONCLUSION
Molecular docking, drug-likeness and pharmacokinetic studies were carried out on twenty-two set of endometrial cancer agents. This study confirmed the endometrial cancer agent's inhibitory activities, their safety through their pharmacokinetic profiles and could be used as potential drugs for the treatment of endometrial or uterine cancer.