2. Materials and methods

#### 2.1 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.

The quinolone compounds have been synthesized by Gould-Jacobs cyclization process (Figure 7). Appropriate unsubstituted aniline (1) is reacted with diethyl

pathogens, such as Staphylococcus aureus, Streptococcus pneumoniae, Moraxella

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

catarrhalis, Haemophilus influenzae, and Mycoplasma pneumoniae.

(Figure 4) and zabofloxacin (Figure 5).

Figure 1. Voreloxin.

Molecular Docking and Molecular Dynamics

Figure 2. Moxifloxacin.

Figure 3. Lascufloxacin.

20

Quinolone derivatives 2D structures 3D optimized structures

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

PQ4:1-allyl-6-fluoro-7-(4-methylpiperidin-1-yl)-1,4-dihydro-4-oxoquinolin-3-carboxylic acid [14]

DOI: http://dx.doi.org/10.5772/intechopen.85970

6ClPQ4:1-allyl-6-chloro-7-(4-methylpiperidin-1-yl)-1,4-dihydro-4-oxoquinolin-3-carboxylic acid [19]

HPQ4:1-allyl-7-(4-methyl-piperidin-1 yl)-1,4-dihydro-4-oxo-quinolin-3-

E: 1171.69431 au

E: 1532.05076 au

carboxylic acid [15] E: 1072.46696 au

acid [16] E: 1111.77842 au

acid [14] E: 1172.93189 au

acid [19] E: 1533.28880 au

acid [16] E: 1113.01581 au

23

E: 1325.35417 au

E: 1073.70428 au

6MePQ4:1-allyl-6-methyl-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

PQ12:1-isopropyl-6-fluoro-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

6ClPQ12:1-isopropyl-6-chloro-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

HPQ12:1-isopropyl-7-(4-methylpiperidin-1-yl)-1,4-dihydro-4-oxoquinolin-3-carboxylic acid [15]

6MePQ12:1-isopropyl-6-methyl-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

PQ11:1-benzyl-6-fluoro-7-(4-methylpiperidin-1-yl)-1,4-dihydro-4-oxoquinolin-3-carboxylic acid [14]

Figure 6.

General structure of the investigated quinolone compounds, where R1 = allyl, isopropyl, benzyl, p-nitro-phenyl, p-amino-phenyl and R6 = F, Cl, H, CH3.

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

ethoxymethylenemalonate (DEEMM) to produce the anilinomethylene malonate derivatives (2). A subsequent thermal process induces Gould-Jacobs cyclization to afford the corresponding 4-hydroxy-quinoline-3-carboxylate ethyl ester (3). The following operation is the alkylation/arylation of the quinolone compound (4), which is usually accomplished by reaction with allyl chloride, benzyl chloride, or para fluoronitrobenzene to produce the qinolone-3-carboxylate ester (4) (R1 = allyl, benzyl, para nitrophenyl) [14–16, 19, 20]. The qinolone-3-carboxylate ester (4) (R1 = isopropyl) was obtained by the reaction of the corresponding monosubstituted aniline (5) (R1 = isopropyl) (the aniline (5) was obtained by reductive amination of acetone with sodium borohydride-acetic acid [14–16, 19] or triacetoxyborohydride [17, 18]) with DEEMM. A strong acid (such as polyphosphoric acid) is often needed to induce cyclization directly resulting in the formation of N-isopropyl-4-oxoquinolone-3-carboxylate ester (4) (R1 = isopropyl).

The final manipulation is the basic or acid hydrolysis that cleave the ester generating the biologically active free carboxylic acid (7) (R1 = allyl, isopropyl, benzyl, para nitrophenyl). The displacement of 7-chloro group from the biologically active free carboxylic acid (7) with 4-methyl-piperidine yielded the compound (8) (R1 = allyl, benzyl, isopropyl, para nitrophenyl) (Table 1). The quinolone compounds (8) (R1 = para amino phenyl) (Table 1) have been synthesized by a common reduction of nitro group using sodium dithionite [20].

#### 2.2 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) In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound DOI: http://dx.doi.org/10.5772/intechopen.85970


ethoxymethylenemalonate (DEEMM) to produce the anilinomethylene malonate derivatives (2). A subsequent thermal process induces Gould-Jacobs cyclization to afford the corresponding 4-hydroxy-quinoline-3-carboxylate ethyl ester (3). The following operation is the alkylation/arylation of the quinolone compound (4), which is usually accomplished by reaction with allyl chloride, benzyl chloride, or para fluoronitrobenzene to produce the qinolone-3-carboxylate ester (4) (R1 = allyl, benzyl, para nitrophenyl) [14–16, 19, 20]. The qinolone-3-carboxylate ester (4) (R1 = isopropyl) was obtained by the reaction of the corresponding monosubstituted aniline (5) (R1 = isopropyl) (the aniline (5) was obtained by reductive amination of acetone with sodium borohydride-acetic acid [14–16, 19] or triacetoxyborohydride [17, 18]) with DEEMM. A strong acid (such as polyphosphoric acid) is often needed to induce cyclization directly resulting in the formation of N-isopropyl-4-oxo-

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

General structure of the investigated quinolone compounds, where R1 = allyl, isopropyl, benzyl, p-nitro-phenyl,

The final manipulation is the basic or acid hydrolysis that cleave the ester generating the biologically active free carboxylic acid (7) (R1 = allyl, isopropyl, benzyl, para nitrophenyl). The displacement of 7-chloro group from the biologically active free carboxylic acid (7) with 4-methyl-piperidine yielded the compound (8) (R1 = allyl, benzyl, isopropyl, para nitrophenyl) (Table 1). The quinolone compounds (8) (R1 = para amino phenyl) (Table 1) have been synthesized by a com-

To achieve the docking studies, the quinolone derivatives (ligands) must be prepared to be imported in the molecular docking project. The ligands (Table 1)

quinolone-3-carboxylate ester (4) (R1 = isopropyl).

2.2 Ligand preparation

22

Figure 6.

Figure 7.

p-amino-phenyl and R6 = F, Cl, H, CH3.

Molecular Docking and Molecular Dynamics

mon reduction of nitro group using sodium dithionite [20].


have been prepared using SPARTAN'14 software package [21] according to the protocol described in our previous work [22]. The DFT/B3LYP/6-31 G\* level of basis set has been used for the computation of molecular structure, vibrational frequen-

Quinolone derivatives 2D structures 3D optimized structures

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

Some chemical properties, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy values, HOMO and LUMO orbital coefficient distribution, molecular dipole moment, polar surface area (PSA) (a descriptor that has been shown to correlate well with passive molecular transport through membranes, therefore, allows the prediction of transport properties of the drugs), the ovality, polarizability (useful to predict the interactions between nonpolar atoms or groups and other electrically charged species, such as ions and polar molecules having a strong dipole moment), and the octanol water partition coeffi-

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

Docking studies have been carried out in order to achieve accurate predictions on the optimized conformations for both the quinolone derivatives (as ligands) and

cies, and energies of optimized structures.

The 2D and 3D structures of the quinolone compounds.

A6ClPQ13: 1-(p-amino-phenyl)-6 chloro-7-(4-methyl-piperidin-1-yl)- 1,4-dihydro-4-oxo-quinolin-3-

DOI: http://dx.doi.org/10.5772/intechopen.85970

AHPQ13:1-(p-amino-phenyl)-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

A6MePQ13:1-(p-amino-phenyl)-6 methyl-7-(4-methyl-piperidin-1-yl)- 1,4-dihydro-4-oxo-quinolin-3 carboxylic acid [20] E: 1281.47987 au

E = energy and au = atomic units.

carboxylic acid E: 1701.75238 au

E: 1242.16807 au

acid

Table 1.

cient (log P) have been calculated (Table 2).

2.3.1 Docking evaluation against human DNA topoisomerase

2.3 Docking studies

proteins.

25

In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound DOI: http://dx.doi.org/10.5772/intechopen.85970


### Table 1.

Quinolone derivatives 2D structures 3D optimized structures

6ClPQ11:1-benzyl-6-chloro-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

Molecular Docking and Molecular Dynamics

HPQ11:1-benzyl-7-(4-methylpiperidin-1-yl)-1,4-dihydro-4-oxoquinolin-3-carboxylic acid [15]

6MePQ11:1-benzyl-6-methyl-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

PQ13:1-(p-nitro-phenyl)-6-fluoro-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

6ClPQ13:1-(p-nitro-phenyl)-6-chloro-7-(4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

HPQ13:1-(p-nitro-phenyl)-7- (4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

6MePQ13:1-(p-nitro-phenyl)-6 methyl-7-(4-methyl-piperidin-1-yl)- 1,4-dihydro-4-oxo-quinolin-3 carboxylic acid [20] E: 430.62213 au

APQ13:1-(p-amino-phenyl)-6-fluoro-7-(4-methyl-piperidin-1-yl)-1,4 dihydro-4-oxo-quinolin-3-carboxylic

E: 1226.12649 au

acid [16] E: 1265.46016 au

acid [20] E: 1490.53723 au

acid [20] E: 1850.89287 au

acid

acid [20] E: 1341.39572 au

24

E: 1391.31010 au

acid [19] E: 1685.71018 au

The 2D and 3D structures of the quinolone compounds.

have been prepared using SPARTAN'14 software package [21] according to the protocol described in our previous work [22]. The DFT/B3LYP/6-31 G\* level of basis set has been used for the computation of molecular structure, vibrational frequencies, and energies of optimized structures.

Some chemical properties, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy values, HOMO and LUMO orbital coefficient distribution, molecular dipole moment, polar surface area (PSA) (a descriptor that has been shown to correlate well with passive molecular transport through membranes, therefore, allows the prediction of transport properties of the drugs), the ovality, polarizability (useful to predict the interactions between nonpolar atoms or groups and other electrically charged species, such as ions and polar molecules having a strong dipole moment), and the octanol water partition coefficient (log P) have been calculated (Table 2).

### 2.3 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.

#### 2.3.1 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


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

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

62.95 and RMSD: 0.08), HPQ11 (score:

RMSD: 0.04) showed better docking score than that of co-crystalized TTC (score: 59.15 and RMSD: 0.14) as shown in Figures 8b–11a. The most active compound,

of all quinolone derivatives in the ligand binding site of human DNA topoisomerase

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

RMSD: 0.32) showed better docking score than that of co-crystalized LFX (score:

(a) Binding site and docking pose of the co-crystallized TTC ligand interacting with the amino acid residues of the ligand binding site of human DNA topoisomerase I. (b) Docking pose of the PQ11 ligand interacting with

the amino acid residues of the ligand binding site of human DNA topoisomerase I.

2.3.2 Docking evaluation against topoisomerase IV from Klebsiella pneumoniae

62.48 and RMSD: 0.01), and 6MePQ13 (score:

63.31 and RMSD:

2.961 Å) (Figure 9a). Docking poses

43.98 and RMSD: 0.05), 6ClPQ4 (score:

42.76 and RMSD: 0.18), and APQ13 (score:

48.32 and RMSD: 0.10), HPQ11 (score: 49.57 and

–15a. The most active compound,

62.77 and RMSD:

63.31) and forms one

61.22 and

41.12

42.96 and

Table 3. Interactions of quinolone derivatives PQ11 (score:

6ClPQ11, was predicted to have a significant docking score (

hydrogen bond with GLU 418 (bond length

DOI: http://dx.doi.org/10.5772/intechopen.85970

.

0.12), 6ClPQ11 (score:

0.06), 6MePQ11(score:

I are shown in Figure 11b

quinolone derivatives PQ4 (score:

37.26 and RMSD: 0.02) as shown in Figures 12b

and RMSD: 0.25), PQ11 (score:

RMSD: 0.11), PQ12 (score:

Figure 8.

27

In Silico Drug Design and Molecular Docking Studies of Some Quinolone Compound DOI: http://dx.doi.org/10.5772/intechopen.85970

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: 63.31 and RMSD: 0.12), 6ClPQ11 (score: 62.95 and RMSD: 0.08), HPQ11 (score: 62.77 and RMSD: 0.06), 6MePQ11(score: 62.48 and RMSD: 0.01), and 6MePQ13 (score: 61.22 and RMSD: 0.04) showed better docking score than that of co-crystalized TTC (score: 59.15 and RMSD: 0.14) as shown in Figures 8b–11a. The most active compound, 6ClPQ11, was predicted to have a significant docking score (63.31) and forms one hydrogen bond with GLU 418 (bond length 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.
