The goal of the study was to forecast the affinities of 10 ligands for the COX-2 target protein as hese compounds were reported to have anti-cancer activities [9]. The more relevant and practical the binding energy would be, the lower its value. The ADME properties of chemical compounds play a critical role in determining how well a medicine works. The difficult and demanding process of drug design and trial can be used to optimize ADME features, which can prevent pharmacokinetics-related failure in clinical stages [22]. Early consideration of ADME during the clinical drug development process has been shown to reduce attrition rates. As a consequence, 10 drugs' early-stage ADME features were evaluated using the SwissADME online tool.
Molecular docking analysis
The molecular docking simulation was used to verify the ketoprofen amides' anticancer properties. The cyclooxygenase isoenzyme target COX-2 (PDB ID: 3Q7D) was docked against ten ligands in order to find potential binding interactions between the ketoprofen amides and the protein. Nine poses were acquired for all docking simulations and were assessed. Ketoprofen amides were successfully docked to the 3Q7D, and modes of interactions with a particular docking score were developed. The inhibitory effects of 10 ligand molecules on cyclooxygenase-2 COX-2 (3Q7D) were assessed in this study. While going through docking, protein (3Q7D) and drug molecules (ligands) do various things based on H-bond, hydrophobic interactions, Van der Waal interactions, and ionic bonds, etc., with their greatest docking score being the most stable for the ligand (Table 2). The RMSD and binding energy measurements are not necessarily the only criteria in molecular docking. Molecular interactions such as ionic bonds, hydrogen bonds, hydrophobic bonds, Van der Waal interactions, and others are also crucial.
The linkage of certain amino acids involved in the interactions between drugs and proteins was also noted. In the active site of 3Q7D, Compound 1 (2-(3-benzoylphenyl)-N-cyclohexylpropanamide) formed H-bonds with Cys-41, Cys-47, and Asn-39, providing a binding affinity of -9.932 kcal/mol. Compound 1 showed some amide-pi stacked interaction with Val-155 (Figure 1).
Compound 2 (2-(3-benzoylphenyl)-N-(3-hydroxypropyl)propanamide) has a binding energy of -7.745 kcal/mol while forming conventional H-bonds with Gln-461 and Asn-39 in the active site of 3Q7D (Figure 2). Compound 2 also formed some pi-alkyl interaction with Arg-44, Arg-469, and Pro-153 along with 1 carbon-hydrogen bond with Arg-469.
Compound 3 (3-(2-(3-benzoylphenyl)propanamido)propanoic acid), showed significant binding, yielding a binding affinity of -8.504 kcal/mol while forming H-bonds with Arg-120 in the active site of 3Q7D. Some amide-pi stacked interaction of compound 3 with Tyr-115, pi-cation with Arg-120, pi-sigma with Val-89 and Val-116, and pi-alkyl with Leu-93 were observed (Figure 3).
Significant binding was achieved by compound 4 (2-(3-benzoylphenyl)-N-propylpropanamide), which formed H-bonds with Arg-120 in the active site of 3Q7D and produced a binding affinity of -8.283 kcal/mol. Compound 4 was shown to have some interactions like pi-alkyl with Tyr-355 and Leu-531, alkyl with Leu-93 and Val-349, pi-sigma with Ala-527 and Val-349, pi-pi T-shaped with Tyr-385 and Trp-387 and pi-sulfur with Met-522 (Figure 4).
Compound 5 (2-(3-benzoylphenyl)-N,N-diethylpropanamide) interacted with 3Q7D with the binding affinity of -7.917 by forming hydrogen bonds with Arg-120 and also formed pi-cation with Arg-120, pi-alkyl with Val-116, pi-sigma with Val-89 and Leu-93 and alkyl with Pro-84, Val-89, and Ile-92 (Figure 5).
By forming H-bonds with Arg-120 and Gln-374, as well as pi-sigma interactions with Leu-145, compound 6 (2-(3-benzoylphenyl)-N-benzylpropanamide), interacted with the 3Q7D with the binding affinity of -9.624 kcal/mol (Figure 6).
Compound 7 (2-(3-benzoylphenyl)-N-cyclohexylpropanamide) bound to 3Q7D with the binding affinity of -8.293 kcal/mol by forming H-bonds with Tyr-115. Besides such strong hydrogen bonding, compound 7 formed pi-sigma interactions with Val-89, Val-116, and Leu-93. Some interaction of compound 7 like pi-alkyl with Leu-93 and Ile-92 and alkyl with Val-89 and Pro-84 were observed (Figure 7).
Compound 8 formed H-bonds with Arg-376 in order to interact with 3Q7D with the binding affinity of -8.88 kcal/mol. Compound 8 also generated pi-pi stacked contacts with Phe-142 in addition to such robust hydrogen bonds. There were some pi-sigma interactions between compound 8 and Leu-145 (Figure 8).
Favorable hydrogen bond interactions between Glu-524 residues in the active site of 3Q7D were seen with compound 9 at the binding affinity of -7.889 kcal/mol. With Val-89, and Leu-93 residues, pi-sigma interactions were found. With Ile-112, Val-116, Leu-93, and Val-89 residues, the pi-alkyl bond type was also seen.
The interactions of the compound 10 (2-(2-(3-benzoylphenyl)propanamido)acetic acid) to the 3Q7D with the binding affinity of -8.641 kcal/mol revealed that residues Arg-120 and Glu-524 showed H-bonds. The residues Val-116, Leu-93, and Val-89 interacted with compound 10 through pi-sigma interaction while Ile-92 and Leu-93 showed pi-alkyl interaction (Figure 10).
ADME and toxicity results
Drug-likeness Prediction
The ligands' aqueous solubility and gut blood barrier permeability, which are connected to their drug-like characteristics, dictate the initial stage of oral bioavailability. Table 1 lists the findings for drug-likeness, bioactivities, ADME, and toxicity profile in the first stage of oral bioavailability. The evaluation of the compounds using Lipinski's Rule of Five. These criteria, which consider molecular weight (Mol wt <500), are used to determine how frequently Lipinski's rule of five has been violated. The topological surface area (TPSA<402Å2), number of hydrogen bond donors (nHBD<5) and acceptors (nHBA< 10), and octanol/water partition coefficient (QP log Po/w = 2:0 - 6:5) were all anticipated. The absence of violations of these rules decreases the likelihood that a molecule will be consumed and is a sign that it is drug-like. No compounds that had broken the guidelines were discovered. The results suggest that the compounds possessed characteristics that could be utilized to create novel medications.
Prediction of Skin Permeability
For drugs meant for topical use, this is crucial. The distribution of the computed skin permeability parameter reveals that every component is within the range that 95% of known medications consider to be acceptable (QPlogKp).
Bioavailability, Lead likeliness, and Synthetic accessibility
The bioavailability score for Ketoprofens was found to be 0.55, indicating a chance of 55% (greater than 10%) for rat bioavailability. While Ketoprofens showed lead resemblance and a high value of synthetic accessibility, Brenk and PAINS both lacked any alarms. The chemicals were found to be drug-like molecules, lipid- and water-soluble, and physiologically active substances.
Ketoprofens' pharmacokinetic characteristics and toxicity were predicted. Table 3 displays the findings of the pharmacokinetic properties and toxicity analysis. For pharmacokinetic properties, solubility and partition coefficient were computed, while mutagenicity, tumorigenicity, irritative impact, and risk of reproductive damage were projected for toxicity studies. Good pharmacokinetic qualities were demonstrated by the in silico pharmacokinetic and toxicology study results. The hydrophilicity of both substances would be determined by the log P value, it was predicted. High log P values have been linked to poor absorption or penetration, and they must be less than 5. According to this analysis, all the substances agreed to this limit. The anticipated pharmacokinetic characteristics and toxicity for a compound's distribution and absorption characteristics are greatly influenced by its water solubility (log S). The estimated log S values for the substances under study fell within the permitted range. The compound's overall potential as a drug candidate was assessed using the drug score formula. It combines the risk parameters for toxicity, molecular weight, clog P, log S, and drug-likeness, and those are provided in the table. The drug score revealed that ketoprofens adhere to all regulations, are not hazardous, and are carcinogenic. This finding further motivates us to find more innovative inhibitors for the treatment of cancer.