Virtual Screening of Phenylenediamine Schiff`s Base Derivatives as Possible DNA Intercalating Agents

There are several ways by which organic compounds can interact
with Deoxyribonucleic Acid (DNA), including covalent bonding...

The vital role of phenylenediamine Schiff bases derivatives as DNA intercalators have been widely described by many research groups. Recently two novel complexes of Schiff bases derived from the condensation of o-phenylenediamine with 3-ethoxysalicylaldehyde have been reported along with their DNA binding, antimicrobial screening and anticancer activities [9,10]. The results demonstrate that the investigated complexes exhibit effective cytotoxicity against growth of carcinoma cells with respect of its imine ligand.
Later in 2019, docking studies of three chromium complexes with o-phenylenediamine as secondary ligands with DNA interaction activity have been described [11]. The kinetic parameters revealed that the binding of the complexes with DNA were surface bindings, mainly due to groove binding. Very recently, our research group reported on the DNA interacting activity of some novel symmetrical ortho-phenylenediamine Schiff's base derivatives. The binding properties of these compounds to genomic DNA (G-DNA) have been investigated indicating that all compounds studied can interact G-DNA [12]. In this work, we aimed to design and predict the DNA intercalating ability of some Schiff's base derivatives obtained from three structural isomers of phenylenediamine using four different DNA fragments as possible intercalating sites.

Consequently, absorption parameters such as Human Intestinal
Absorption, Blood Brain Barrier, P-glycoprotein interaction (substrate or inhibitor) and metabolism (inhibitor or substrate) of the bio-active molecules with different cytochrome P450 enzymes were also estimated using ADMET-SAR, which is based on QSAR data for prediction of Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) [14,15]. Drug-like molecules considering Lipinski rules and good ADMET properties were chosen as ligands in consequent molecular docking procedures.

Molecular Docking
The starting geometry of all investigated compounds was

Designing and Preparation of Phenylenediamine Derivatives Compounds
The starting geometry of all investigated compounds was constructed using Chem3D Ultra (version 12.0, Cambridge soft Com., USA) as described in DNA optimization. The optimized geometry of tested compounds with the lowest energy was used in the molecular dockings. In addition, the discovery studio visualizer was used for all tested compounds and converted to PDB files and used as input in PyRx software.

Docking Process and Analysis
The DNA crystal structure used in this investigation was loaded in PyRx virtual screening tool as pdbqt format. The standard drug and designed compoundspdb files were loaded and automatically converted to pdbqt format. The docking was performed with autodockvina. The centersand the dimensions of the grid box were assigned for each DNA segment as described in Table 1. The best free energy of binding values was obtained and the best interactions were visualized by Discovery Studio.

Design Of Phenylenediamine Schiff's Base Derivatives
Based on the importance of phenylenediamine Schiff's base derivatives as DNA intercalators as described in the introduction part, and because of their versatile route of chemical synthesis, the three structural isomers of phenylenediamine were used to develop a series of aromatic imino analogues. Comparing the 3-D structures of ortho, meta and para isomers phenylenediamine Schiff's base derivates indicate that meta and para isomers are more planar than the ortho isomer. This could be attributed to the increased steric interaction of the two imino substituents in ortho positions.

ADMET Properties
The pharmacokinetic properties of all investigated compounds were studied using Lipinski's rule of five and toxicity. All

Reference Compounds
Two well-known biologically active DNA intercalating agents were used as references (Figure 1), namely paclitaxel (taxol) and the aureolic acid group antitumor drug, UCH9. Taxol is considered a successful drug in the treatment of various forms of cancers [17][18][19]. UCH9 contains more hydrophilic parts (polyhydroxyl groups) and longer hydrophobic side chains (aromatic rings). Both of the compounds bind to the minor groove of DNA and cause DNA unwinding. The docking energy of both reference compounds against the tested DNA fragments is depicted in Table 2.

Discussion of Docking Results of Series I Compounds
Based on the results of series I phenylenediamine Schiff's base derivatives, we predict an increased DNA intercalating efficacy for all series I derivatives. This prediction was confirmed since the docking energy of all derivatives are less than the corresponding phenylenediamine isomer, which may be attributed to the introduction of extra aromatic rings to the unsubstituted phenylenediamine isomer. In general, the di-substituted isomer of phenylenediamine is more active than the corresponding monosubstituted isomer except for ortho isomers, which is probably due to steric obstruction affecting the planarity of the three aromatic rings ( Figure 2). In addition, meta isomers are the most active among the three isomers, whereas para isomers are generally more active than ortho isomers. Introduction of hydrophilic substitutes (R) to the aromatic ring of either monosubstituted or di-substituted derivatives leads to a decrease of the intercalating efficacy, viz.    Comparing the localization of the three isomers of di-2hydroxynaphthyl analogues (ortho (BNA208), meta (BNB208), and para (BNC208)), as shown in Figure 5, indicate that both meta and para isomers which show increased efficacy, when compared with ortho isomers, are located at the same location within the intercalating site (minor groove of DNA), whereas the ortho isomer has a twisted shape as result of its non-planarity. Investigation of the interaction of BNB2028 (meta isomer) with the DNA intercalating site shows that only one of the two hydroxyl groups is involved in formation of a hydrogen bond with the DNA nucleotide as donor.
The other hydroxyl group is involved in intramolecular hydrogen bonding with the azomethine group.

Series (II): Only disubstituted isomers ofphenylenediamine
were investigated in our study, because the results obtained from series I compounds indicated that they are more active than the corresponding monosubstituted isomers. In this series, the most active derivative from each group was used as a lead structure to design the following group to develop more active analogues.  Table 4.

Discussion of Docking Results of Group D Compounds
Comparing   Table 5.

Discussion of Docking Results of Group E Compounds
The

Group F: Lipophilic Analogues of Disubstituted Hydroxyl and Nitro Naphthyl Phenylenediamine Derivatives
The strategy which applied to design this group was based on substitution of nitro groups of compound BNE402 (the most active of group E) with non-hydrogen bonding lipophilic groups. In addition, the effect of replacing of the naphthyl ring with a three ring system (anthracene or phenantrene) was also investigated. The chemical structures, partition coefficient, hydrogen bond ability and docking energies of group F derivatives are listed in Table 6.

Discussion of Docking Results of Group E Compounds
Most   Table 7. The analogues which contain 4-methyl or 4-chloro (lipophilic) groups have nearly equal activities for 1-naphthyl and2-naphthyl derivatives as summarized in Figure 9.The main difference in the DNA intercalation of both 1-naphthyl and 2-naphthyl derivatives can be \attributed to the difference in the localization within the intercalating site, where 2-naphthyl derivatives occupy a larger space than 1-naphthyl derivatives.  Our docking results are consistent with five Schiff base ligands that were synthesized and fully spectroscopically characterized.
The five Schiff base ligands which contain stronger electron donating substituents had higher DNA-binding ability than the nonelectron donating analogues [20]. The molecular docking results of the five Schiff base ligands showed that all of the synthesized ligands were minor groove binders and the H-bond interactions play a dominant role in the stability of ligand-DNA [20]. In addition, another binding study of a series of p-dimethylaminobenzaldehyde and Pseudomonas aeruginosa, using the disc diffusion method.
All the tested Schiff bases compounds showed promising effects against the tested bacterial strains [21]. Two previous studies are consistent with our results which renders our designed compounds promising drugs against some tumours and bacterial strains.

Conclusion
We intercalating efficacy achieved in the current study (compound BNG702), which is, therefore, considered the most promising lead compound in the production of potent DNA-intercalators. In conclusion, we highly recommend the synthesis and in vitro testing of meta phenylenediamine Schiff`s base derivatives with two rings (naphthyl) together with a three (anthracene) ring system.