Serap Yilmaz

Synthesis and Biological Evaluation of 2-Substituted-5-(4-nitrophenylsulfonamido)benzoxazoles as Human GST P1-1 Inhibitors, and Description of the Binding Site Features

Glutathione‐S‐transferases (GSTs) are enzymes involved in cellular detoxification by catalyzing the nucleophilic attack of glutathione (GSH) on the electrophilic center of numerous of toxic compounds and xenobiotics, including chemotherapeutic drugs. Human GST P1‐1, which is known as the most prevalent isoform of the mammalian cytosolic GSTs, is overexpressed in many cancers and contributes to multidrug resistance by directly conjugating to chemotherapeutics. It is suggested that this resistance is related to the high expression of GST P1‐1 in cancers, thereby contributing to resistance to chemotherapy. In addition, GSTs exhibit sulfonamidase activity, thereby catalyzing the GSH‐mediated hydrolysis of sulfonamide bonds. Such reactions are of interest as potential tumor‐directed prodrug activation strategies. Herein we report the design and synthesis of some novel sulfonamide‐containing benzoxazoles, which are able to inhibit human GST P1‐1. Among the tested compounds, 2‐(4‐chlorobenzyl)‐5‐(4‐nitrophenylsulfonamido)benzoxazole (5 f) was found as the most active hGST P1‐1 inhibitor, with an IC50 value of 10.2 μM, showing potency similar to that of the reference drug ethacrynic acid. Molecular docking studies performed with CDocker revealed that the newly synthesized 2‐substituted‐5‐(4‐nitrophenylsulfonamido)benzoxazoles act as catalytic inhibitors of hGST P1‐1 by binding to the H‐site and generating conjugates with GSH to form S‐(4‐nitrophenyl)GSH (GS–BN complex) via nucleophilic aromatic substitution reaction. The 4‐nitrobenzenesulfonamido moiety at position 5 of the benzoxazole ring is essential for binding to the H‐site and for the formation of the GST‐mediated GSH conjugate.

Binding site feature description of 2-substituted benzothiazoles as potential AcrAB-TolC efflux pump inhibitors in E. coli.

The resistance-nodulation-division (RND) family efflux pumps are important in the antibiotic resistance of Gram-negative bacteria. However, although a number of bacterial RND efflux pump inhibitors have been developed, there has been no clinically available RND efflux pump inhibitor to date. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combinations with ciprofloxacin (CIP) against the AcrAB-TolC overexpressor Escherichia coli AG102 clinical strain. The results indicated that the BSN compounds did not show intrinsic antimicrobial activity when tested alone. However, when used in combinations with CIP, a reversal in the antibacterial activity of CIP with up to 10-fold better MIC values was observed. In order to describe the binding site features of these BSN compounds with AcrB, docking studies were performed using the CDocker method. The performed docking poses and the calculated binding energy scores revealed that the tested compounds BSN-006, BSN-023, and BSN-004 showed significant binding interactions with the phenylalanine-rich region in the distal binding site of the AcrB binding monomer. Moreover, the tested compounds BSN-006 and BSN-023 possessed stronger binding energies than CIP, verifying that BSN compounds are acting as the putative substrates of AcrB.

Pharmacophore generation of 2-substituted benzothiazoles as AdeABC efflux pump inhibitors in A. baumannii

RND family efflux pumps are important for multidrug resistance in Gram-negative bacteria. To date no efflux pump inhibitors for clinical use have been found, so developing the specific inhibitors of this pump system will be beneficial for the treatment of infections caused by these multidrug-resistant pathogens. A set of BSN-coded 2-substituted benzothiazoles were tested alone and in combination with ciprofloxacin (CIP) against the RND family efflux pump AdeABC overexpressor Acinetobacter baumannii SbMox-2 strain. The results indicated that the BSN compounds did not have antimicrobial activity when tested alone. However, if they were applied in combination with CIP, it was observed that the antibiotic had antimicrobial activity against the tested pathogen, possessing a minimum inhibitory concentration value that could be utilized in clinical treatment. A 3D-common features pharmacophore model was applied by using the HipHop method and the generated pharmacophore hypothesis revealed that the hydrogen bond acceptor property of nitrogen in the thiazole ring and the oxygen of the amide substituted at the second position of the benzothiazole ring system were significant for binding to the target protein. Moreover, three hydrophobic aromatic features were found to be essential for inhibitory activity.

Quantum mechanical and spectroscopic (FT-IR, FT-Raman, 1H NMR and UV) investigations of 2-(p-nitrobenzyl) benzoxazole

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 2(p-nitrobenzyl)benzoxazole have been investigated experimentally and theoretically using Gaussian09 software package. Potential energy distribution of the normal modes of vibrations are done using GAR2PED program. The optimized geometrical parameters are in agreement with that of similar derivatives. The energy and oscillator strength calculated by Time Dependent Density Functional Theory results almost compliments with experimental findings. Gauge-including atomic orbital H NMR chemical shifts calculations were carried out by using B3LYP functional with 6-31G basis sets. The HOMO and LUMO analysis is used to determine the charge transfer with in the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. MEP was performed by the DFT method and the infrared and Raman intensities have also been reported. Mulliken’s net charges have been calculated and compared with the atomic natural charges. The calculated first hyperpolarizability of the title compound is 82.31 time that of the standard NLO material urea and hence is an attractive object for future studies of nonlinear optical properties. 2013 Elsevier B.V. All rights reserved.

Insight into eukaryotic topoisomerase II-inhibiting fused heterocyclic compounds in human cancer cell lines by molecular docking

Etoposide is effective as an anti-tumour drug by inhibiting eukaryotic DNA topoisomerase II via establishing a covalent complex with DNA. Unfortunately, its wide therapeutic application is often hindered by multidrug resistance (MDR), low water solubility and toxicity. In our previous study, new derivatives of benzoxazoles, benzimidazoles and related fused heterocyclic compounds, which exhibited significant eukaryotic DNA topoisomerase II inhibitory activity, were synthesized and exhibited better inhibitory activity compared with the drug etoposide itself. To expose the binding interactions between the eukaryotic topoisomerase II and the active heterocyclic compounds, docking studies were performed, using the software Discovery Studio 2.1, based on the crystal structure of the Topo IIA-bound G-segment DNA (PDB ID: 2RGR). The research was conducted on a selected set of 31 fused heterocyclic compounds with variation in structure and activity. The structural analyses indicate coordinate and hydrogen bonding interactions, van der Waals interactions and hydrophobic interactions between ligands and the protein, as Topo IIA-bound G-segment DNA are responsible for the preference of inhibition and potency. Collectively, the results demonstrate that the compounds 1a, 1c, 3b, 3c, 3e and 4a are significant anti-tumour drug candidates that should be further studied.

Genotoxic potentials and eukaryotic DNA topoisomerase I inhibitory effects of some benzoxazine derivatives

Benzoxazines are heterocyclic compounds which have been used as intermediates in the synthesis of many heterocyclic structures of biological importance as it has been reported that some of the benzoxazines were effective in promoting apoptosis and inhibiting cell proliferation. Present study contains experimental data that showed genotoxic potentials and inhibitory effects on eukaryotic DNA topoisomerase I of 16 newly synthesized benzoxazine derivatives. By rec assay, the bacterial genotoxicity assay, only four tested compounds were found genotoxic at different concentrations and four compounds showed reverse effect. RC50 values evaluated by rec assay revealed that BS5 was the most genotoxic and BS4 was the most cytotoxic compound at micromolar concentration. Compounds were also tested for their inhibitory effects on eukaryotic DNA topoisomerase I enzyme and it was found that 14 of the compounds had inhibitory effects on eukaryotic DNA topoisomerase I enzyme. The most active compounds, BS18 and BS4, showed higher inhibitory activities than the positive control drug camptothecin which is a well-known commercial topoisomerase I inhibitor.

Generated 3D-common feature hypotheses using the HipHop method for developing new topoisomerase I inhibitors.

The continued interest in designing novel topoisomerase I (Topo I) inhibitors and the lack of adequate ligand‐based computer‐aided drug discovery efforts combined with the drawbacks of structure‐based design prompted us to explore the possibility of developing ligand‐based three‐dimensional (3D) pharmacophore(s). This approach avoids the pitfalls of structure‐based techniques because it only focuses on common features among known ligands; furthermore, the pharmacophore model can be used as 3D search queries to discover new Topo I inhibitory scaffolds. In this article, we employed the HipHop module using Discovery Studio to construct plausible binding hypotheses for clinically used Topo I inhibitors, such as camptothecin, topotecan, belotecan, and SN‐38, which is an active metabolite of irinotecan. The docked pose of topotecan was selected as a reference compound. The first hypothesis (Hypo 01) among the obtained 10 hypotheses was chosen for further analysis. Hypo 01 had six features, which were two hydrogen‐bond acceptors, one hydrogen‐bond donor, one hydrophob aromatic and one hydrophob aliphatic, and one ring aromatic. Our obtained hypothesis was checked by using some of the aromathecin derivatives which were published for their Topo I inhibitory potency. Moreover, five structures were found to be possible anti‐Topo I compounds from the DruglikeDiverse database. From this research, it can be suggested that our model could be useful for further studies in order to design new potent Topo I‐targeting antitumor drugs.

Synthesis and investigation of binding interactions of 1,4-benzoxazine derivatives on topoisomerase IV in Acinetobacter baumannii

Abstract Acinetobacter baumannii has emerged as an important pathogen for nosocomial infections having high morbidity and mortality. This pathogen is notorious for antimicrobial resistance to many common antimicrobial agents including fluoroquinolones, which have both intrinsic and acquired resistance mechanisms. Fluoroquinolones targeting the bacterial topoisomerase II (DNA gyrase and Topo IV) show potent broad-spectrum antibacterial activity by the stabilization of the covalent enzyme–DNA complex. However, their efficacy is now being threatened by an increasing prevalence of resistance. Fluoroquinolones cause stepwise mutations in DNA gyrase and Topo IV, having alterations of their binding sites. Furthermore, the water–Mg+2 bridge, which provides enzyme–fluoroquinolone interactions, has a significant role in resistance. In this study, 13 compounds were synthesized as 1,4-benzoxazine derivatives which act as bacterial topoisomerase II inhibitors and their antibacterial activities were determined against multi-drug resistant Acinetobacter strains which have ciprofloxacin (CIP) resistant and GyrA mutation. Afterwards we performed docking studies with Topo IV (pdb:2XKK) of these compounds to comprehend their binding properties in Discovery Studio 3.5. The results of this study show significant conclusions to elucidate the resistance mechanism and lead to the design of new antibacterial agents as bacterial topoisomerase II inhibitors.