In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound

Quinolones are an important class of heterocyclic compounds that possess interesting biological activities like antimicrobial, antitubercular, and antitumor. The objective of this study is to evaluate in silico the antitumoral and antimycobacterial activity of some quinolone derivatives by using CLC Drug Discovery Workbench Software. Docking studies were carried out for all ligands, and the docking scores were compared with the scores of standard drugs, topotecan and levofloxacin. The docking studies have been carried out to predict the most possible type of interaction, the binding affinities, and the orientations of the docked ligands at the active site of the target protein.

Lascufloxacin Quinolones, considered to be "privileged building blocks," are obtained through simple and flexible synthesis methods and allow design and development of large libraries of bioactive molecules. A 2011 study on 21 antibiotics launched since 2000 has highlighted that the discovery and development of new antibiotics obtained through chemical synthesis is still topical. Of the nine antibiotics obtained by chemical synthesis, launched between 2000 and 2011, eight antibiotics belong to the class of fluoroquinolones [11]. New drugs introduced into medical therapies each year are privileged structures for specific biological targets. These new chemical entities provide a perspective on molecular recognition, serving as a basis for designing future new drugs. In 2016, 19 chemically synthesized drugs were approved [12], with the two drugs having the quinolone structure: nemonoxacin ( Figure 4) and zabofloxacin ( Figure 5).   The objective of this study is to evaluate "in silico" antitumoral and antimycobacterial activities of some quinolone derivatives by using CLC Drug Discovery Workbench Software [13]. Docking studies were conducted for all ligands, and the docking scores were compared with the scores of standard drugs, topotecan and levofloxacin.

Structure and the synthesis pathway of the quinolone derivatives
In previous papers, we presented the synthesis of quinolone derivatives with antimicrobial activity [1,2]. The results have revealed that the compounds represented in Figure 6 have showed weak antibacterial activities against the tested strains. For this reason, we have initiated in silico drug design and molecular docking studies to predict anticancer and antitubercular activities targeting DNAtopoisomerase I and topoisomerase IV from Klebsiella pneumoniae, respectively.
We have performed molecular docking studies to see how the nature of substituents on the quinolone ring influences the anticancer and antitubercular activities targeting human DNA topoisomerase I and topoisomerase IV from Klebsiella pneumoniae, respectively. The studies have been realized with CLC Drug Discovery Workbench Software [13] in order to achieve accurate predictions on optimized conformations for both the quinolones (as ligands) and their target receptor proteins to form stable complexes.

Ligand preparation
To achieve the docking studies, the quinolone derivatives (ligands) must be prepared to be imported in the molecular docking project. The ligands (Table 1) Figure 6. General structure of the investigated quinolone compounds, where R 1 = allyl, isopropyl, benzyl, p-nitro-phenyl, p-amino-phenyl and R 6 = F, Cl, H, CH 3 .

Figure 7.
The synthesis of the quinolone compound using Gould-Jacobs cyclization process.

Docking studies
The docking protocol was performed according to the CLC Drug Discovery Workbench Software and was described in a previous paper [22]. The docking scores and hydrogen bonds formed with the amino acids from group interaction atoms were used to predict the binding modes, the binding affinities, and the orientation of the docked quinolone derivatives in the active site of the target proteins.

Docking evaluation against human DNA topoisomerase
Docking studies have been carried out in order to achieve accurate predictions on the optimized conformations for both the quinolone derivatives (as ligands) and Quinolone derivatives 2D structures 3D optimized structures A6ClPQ13: 1-(p-amino-phenyl)-6chloro-7-(4-methyl-piperidin-1-yl)-1,4-dihydro-4-oxo-quinolin-3carboxylic acid E: À1701.75238 au [20] E: À1281.47987 au E = energy and au = atomic units. protein target to form a stable complex. All of the investigated compounds have been docked on the crystal structure of human DNA topoisomerase I (PDB ID: 1K4T) [23]. Binding site and docking pose of the co-crystallized topotecan (TTC), interacting with amino acid residues of the active site, are shown in Figure 8a. The TTC was taken as reference ligand to compare the docking results of quinolone derivatives. The docking score, the interacting group, and hydrogen bonds formed with the group interaction atoms of the corresponding amino acids are shown in Table 3. Interactions of quinolone derivatives PQ11 (score: À63.31 and RMSD: 0.12), 6ClPQ11 (score: À62.95 and RMSD: 0.08), HPQ11 (score: À62.77 and RMSD: 0.06), 6MePQ11(score: À62.48 and RMSD: 0.01), and 6MePQ13 (score: À61.22 and RMSD: 0.04) showed better docking score than that of co-crystalized TTC (score: À59.15 and RMSD: 0.14) as shown in Figures 8b-11a. The most active compound, 6ClPQ11, was predicted to have a significant docking score (À63.31) and forms one hydrogen bond with GLU 418 (bond length À 2.961 Å) (Figure 9a). Docking poses of all quinolone derivatives in the ligand binding site of human DNA topoisomerase I are shown in Figure 11b.

Docking evaluation against topoisomerase IV from Klebsiella pneumoniae
Docking studies have been carried out in order to obtain optimized docking conformations of the investigated quinolone derivatives on the crystal structure of topoisomerase IV (PDB ID: 5EIX) from Klebsiella pneumoniae [24]. The binding site and docking pose of the co-crystallized levofloxacin (LFX) ligand, interacting with amino acid residues of the ligand binding site of topoisomerase IV from Klebsiella pneumoniae, are shown in Figure 12a. The levofloxacin was taken as reference ligand to compare the docking results of quinolone derivatives. The docking score, the interacting group, and hydrogen bonds formed with the group interaction atoms of the corresponding amino acids are shown in Table 4. Interactions of quinolone derivatives PQ4 (score: À43.98 and RMSD: 0.05), 6ClPQ4 (score: À41.12 and RMSD: 0.25), PQ11 (score: À48.32 and RMSD: 0.10), HPQ11 (score: 49.57 and RMSD: 0.11), PQ12 (score: À42.76 and RMSD: 0.18), and APQ13 (score: À42.96 and RMSD: 0.32) showed better docking score than that of co-crystalized LFX (score: 37.26 and RMSD: 0.02) as shown in Figures 12b-15a. The most active compound,  HPQ11, was predicted to have a significant docking score (À49.57) and forms one hydrogen bond with ASP95 (bond length À 3.081 Å) (Figure 14a). Docking poses of all quinolone derivatives in the ligand binding site of topoisomerase IV from Klebsiella pneumoniae are shown in Figure 15b.  Table 3.
List of docking interactions between the ligand molecules and human DNA topoisomerase I using CLC Drug Discovery Workbench Software.  Important molecular properties of the investigated compounds, e.g., molecular weight, flexible bonds, the number of hydrogen bond donors, the number of hydrogen bond acceptors, and log P, have been calculated. These parameters can be used to evaluate whether a molecule has properties that would make it a likely orally active drug, according to the Lipinski's rule of five [22]. The number of violations of the Lipinski rules allows to evaluate drug likeness for a molecule ( Table 5).

Results and discussions
All of the investigated compounds have been docked on human DNA topoisomerase (PDB ID: 1K4T) and topoisomerase IV (PDB ID: 5EIX) from Klebsiella    Table 4.

Conclusions
The virtual screening of the investigated compounds using docking has been carried out with CLC Drug Discovery Workbench Software and has led to the identification of quinolone derivatives for inhibiting the activities of topoisomerase I and topoisomerase IV. It was observed that the presence of the benzyl substituent in N1 position of the 7-(4-methyl-piperidinyl)-quinolones core leads to increased docking score against human DNA topoisomerase and topoisomerase IV from Klebsiella pneumoniae.