A Computational Approach to Investigate the Biochemical Properties of Paracetamol and Its Metabolites

Paracetamol (PCT) is a mostly used analgesic and antipyretic
drug [1]. Overdoses can cause of liver and kidney damage [2]. The
primary metabolism of PCT occurred in the liver...


Computational Details
Initial geometry of Paracetamol and its metabolites were collected from online chemical structure database named ChemSpider [9] and geometry optimization done by Gaussin03 software [10].
Density functional theory (DFT) along with B3LYP/6-31G basis set has been employed to optimize the geometry. Molecular orbital fea- The 3D structure of prostaglandin synthase protein (PDB ID: 5F19) was obtained in pdb format from online protein data bank (PDB) database [11]. All hetero atoms, water molecules, and inactive chain were erased by using PyMol (version 1.3) software packages [12]. The energy minimization of protein was done by Swiss-Pdb viewer software (version 4.1.0) [13]. Finally, the docking simulation was performed by PyRx software (version 0.8 ) [14] considering the protein as macromolecule and drug as ligand with the center grid box size 20.8612, 37.5501 and 59.3402 Å along x, y and z directions respectively. AdmetSAR online database was utilized to predict the absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of all metabolites [15].

Result and Discussion
Thermodynamic Analysis Thermodynamic properties such as enthalpy of formation and Gibb's free energy of a reaction help us to predict the spontaneity of the reaction and stability of PCT metabolites [16]. Free energy is a crucial criterion to represent the interaction of binding partners where both the sign and magnitude are important to express the prospect of biomolecular incidents occurring [17].  (Table 1). and NAPQI (0.5860) show higher softness, which may contribute to their chemical activity and polarizability than PCT (0.3739) ( Figure   2).

Molecular Docking and ADMET Analysis
Binding affinities are summarized in Table 3. Greater negative values of binding affinity indicate stronger binding between the receptor protein and the PCT metabolites. The binding affinity of PCT is -6.5 kcal/mol. After sulphate conjugation, the binding affinity of the metabolite PCT-S has increased to -6.9 kcal/mol and glucuronide conjugation in metabolite PCT-G has also increased its binding

Pharmacokinetic Properties
Admet SAR online database was utilized for the prediction of absorption, inhibition, metabolism and toxicity of paracetamol metabolites [21]. Presumed pharmacokinetic values are listed below in Table 3. The calculation predicts all PCT metabolites are non-carcinogenic except PCT-S, which is the primary metabolite of PCT by sulphate conjugation by sulfotransferase enzyme, and in particular, its production is not significantly higher after oral administration. All the PCT metabolites possess category III oral toxicity, so the metabolites can be predicted to be relatively harmless in case of oral administration [22]. The metabolites show positive response for blood brain barrier (BBB) issue and predict that metabolites will go through BBB easily. NAPQI is predicted to be non-carcinogenic and has positive value in BBB and intestinal absorption but is has higher toxicity level than other metabolites but due to its small amount of production, it is detoxified by conjugation of glutathione and it's depletion also reduces the capacity to detoxify N-acetyl-pbenzoquinone imine (NAPQI), the toxic metabolite of acetaminophen (PCT) [23]. In the evaluation of acute oral toxicity of PCT metabolites, it is observed that it possesses category III oral toxicity. However, metabolites of PCT have shown weak inhibition of Human Ether-a-go-go-Related Gene (hERG). Inhibition of hERG can lead to long QT syndrome, so further analysis on this aspect is necessary. All the metabolites are non-inhibitor of P-glycoprotein, which is also known as multidrug resistance protein-1.

Conclusion
All the metabolites of PCT are thermally and configurationally The metabolites are weak inhibitor for hERG.