Platinum(II) compounds with chelating ligands based on pyridine and pyrimidine: Synthesis, characterizations, DFT calculations, cytotoxic assays and binding to a DNA model base

Two chelating ligands based on secondary amines have been selected to prepare four new Pt(II) compounds. The ligands bis(pyridine-2-yl)amine, abbreviated dpa, and bis(pyrimidine-2-yl)amine, abbreviated dipm, are chosen to design a rigid chelating motif to allow the study of subtle differences in electronic properties and hydrogen bonding ability. Different carrier ligands (i.e. chloride and ammine) have also been introduced to allow a study of structure–activity relationships. Two of the four compounds are cisplatin analogues, whereas the other two are cationic and coordinatively saturated compounds. The four synthesized and characterized compounds are [Pt(dpa)Cl₂], [Pt(dpa)(NH₃)₂](NO₃)₂, [Pt(dipm)Cl₂] and [Pt(dipm)(NH₃)₂](NO₃)₂ with code numbers C1–C4. The spatial structures of all these compounds have also been optimized using DFT (density functional theory) calculations. The cytotoxicity of these compounds has been investigated in seven human tumor cell lines using the SRB (sulforhodamine B) assay. The most promising antitumor active compound appears to be C3, [Pt(dipm)Cl₂]. Two water-soluble compounds, C2 and C4 exhibit selective activity in EVSA-T cell line. In addition, the reaction of the cisplatin analogues with the model base 9-ethylguanine has been followed by proton and platinum NMR spectroscopy.     

Preparation and characterization of N-(3-pyridinyl) spirocyclic diamines as ligands for nicotinic acetylcholine receptors

Several N-pyridin-3-yl spirobicyclic diamines, designed as conformationally restricted analogs of tebanicline (ABT-594), were synthesized as novel ligands for nicotinic acetylcholine receptors (nAChR). The spirocyclic compounds exhibited weaker binding affinity, than other constrained analogs in accord with a pharmacophore model. Nevertheless, some (1a, 1b) possessed (partial) agonist potencies comparable to nicotine at the α4β2 subtype, but with greatly improved selectivity relative to the α3β4* nAChR.     

Pharmacological properties and predicted binding mode of arylmethylene quinuclidine-like derivatives at the α3β4 nicotinic acetylcholine receptor (nAChR)

We have carried out a pharmacological evaluation of arylmethylene quinuclidine derivatives interactions with human α3β4 nAChRs subtype, using cell-based receptor binding, calcium-influx, electrophysiological patch-clamp assays and molecular modeling techniques. We have found that the compounds bind competitively to the α3β4 receptor with micromolar affinities and some of the compounds behave as non-competitive antagonists (compounds 1, 2 and 3), displaying submicromolar IC₅₀ values. These evidences suggest a mixed mode of action for these compounds, having interactions at the orthosteric site and more pronounced interactions at an allosteric site to block agonist effects. One of the compounds, 1-benzyl-3-(diphenylmethylene)-1-azoniabicyclo[2.2.2]octane chloride (compound 3), exhibited poorly reversible use-dependent block of α3β4 channels. We also found that removal of a phenyl group from compound 1 confers a partial agonism to the derived analog (compound 6). Introducing a hydrogen-bond acceptor into the 3-benzylidene quinuclidine derivative (compound 7) increases agonism potency at the α3β4 receptor subtype. Docking into the orthosteric binding site of a α3β4 protein structure derived by comparative modeling accurately predicted the experimentally-observed trend in binding affinity. Results supported the notion that binding requires a hydrogen bond formation between the ligand basic nitrogen and the backbone carbonyl oxygen atom of the conserved Trp-149.     

MiR-34a promotes Fas-mediated cartilage endplate chondrocyte apoptosis by targeting Bcl-2

Seven organorhenium pentylcarbonate compounds (PC1–PC7) have been synthesized. DNA-binding studies of the PC-series compounds using electronic spectroscopy and gel electrophoresis suggest that the compounds presumably bind to DNA in an intercalative mode. The intrinsic binding constants for PC4, PC6, and PC7 were found to be 1.6 × 10⁴, 3.9 × 10⁴, and 4.2 × 10⁴ M^?1, respectively. The X-ray structure determinations and density functional theory calculations indicate that the polypyridyl ligands in the compounds are nearly planar facilitating DNA binding through an intercalation mechanism. Cytotoxicity studies of 10 µM pentylcarbonate compounds against HTB-12 human astrocytoma brain cancer cells were studied for 48 h. It was observed that each of the pentylcarbonate compounds is active against the cancer cells. However, under analogous conditions, CRL-2005 rat astrocyte normal brain cells are not affected significantly.     

Rh(I) complexes containing tris(pyrazolyl)amine and bis(pyrazolyl)amine ligands: synthesis and NMR studies

The tris(pyrazolyl)amine ligands: tris[2-(1-pyrazolyl)methyl]amine (tpma), tris [3,5-dimethyl-1-pyrazolyl)methyl]amine (tdma), tris[2-(1-pyrazolyl)ethyl]amine (tpea), tris[2-(3,5-dimethyl-1-pyrazolyl)ethyl]amine (tdea) and bis(pyrazolyl)amine ligands: bis[2-(1-pyrazolyl)ethyl]amine (bpea) and bis[2-(3,5-dimethyl-1-pyrazolyl)ethyl]amine (bdea) react with [RhCl(cod)]₂ in presence of NaBF₄ (tpma, tdma and bdea) or AgBF₄ (tpea, tdea and bpea) to lead to [Rh(cod)L] (BF₄) (L=tpma (1), tdma (2), bdea (3), tpea (4), tdea (5) and bpea (6)). These complexes have been characterised by elemental analyses, conductivity, IR, ¹H and ¹³C NMR spectroscopy and liquid mass (with electrospray) spectrometry. The ¹H NMR spectra of 1, 2 show the presence of two isomers in solution in a 3:1 ratio (coordination κ² or κ³ type) in a thermodynamic equilibrium. The steric bulk of cyclo-octa-1,5-diene causes it to prefer the κ² mode of bonding as majority. Similar to previous published results, complexes 4 and 5 exist in a sole form in solution (probably κ² isomer). Finally, the complexes 3 and 6 are fluxional. A NMR study shows that this fluxional process is not frozen at 183 K.     

Synthesis,biological activity and multiscale molecular modeling studies of bis-coumarins as selective carbonic anhydrase IX and XII inhibitors with effective cytotoxicity against hepatocellular carcinoma

A series of novel bis-coumarin derivatives containing triazole moiety as a linker between the alkyl chains was synthesized and their inhibitory activity against the human carbonic anhydrase (hCA) isoforms I, II, IX and XII were evaluated. In addition, cytotoxic effects of the synthesized compounds on renal adenocarcinoma (769P), hepatocellular carcinoma (HepG2) and breast adeno carcinoma (MDA-MB-231) cell lines were examined. While the hCA I and II isoforms were inhibited in the micromolar range, the tumor-associated isoform hCA IX and XII were inhibited in the high nanomolar range. 4-methyl-7-((1-(12-((2-oxo-2H-chromen-7-yl)oxy)dodecyl)-1H-1,2,3-triazol-4-yl)methoxy)-2H-chromen-2-one (5p) showed the strongest inhibitory activity against hCA IX with the K_i of 144.6 nM and 4-methyl-7-((1-(10-((2-oxo-2H-chromen-7-yl)oxy)decyl)-1H-1,2,3-triazol-4-yl)methoxy)-2H-chromen-2-one (5n) exhibited the highest hCA XII inhibition with the K_i of 71.5 nM. In order to better understand the inhibitory profiles of studied molecules, multiscale molecular modelling approaches were applied. Low energy docking poses of studied molecules at the binding sites of targets have been predicted. In addition, electrostatic potential surfaces (ESP) for binding sites were also generated to understand interactions between proteins and active ligands.     

Self-assembled pentagonal bipyramidal and skew trapezoidal organotin(IV) complexes of substituted benzoic acids: Their antibacterial, antifungal, cytotoxic, insecticidal and urease inhibition activities

Fourteen di- and triorganotin(IV) derivatives with pentagonal bipyramidal and skew trapezoidal geometries have been synthesized and characterized. Dimethylstannyl bis[3-amino-4-chlorophenylcarboxylate] (1), bis[3-amino-4-chlorophenylcarboxylato] tetraethyldistannoxane] (2) and bis[3,5-dinitro-4-chlorophenylcarboxylato] tetra-n-butyldistannoxane (10) are dinuclear and tetranuclear complexes of bidentate ligands. The crystal structure of (1) is dimeric in which each Sn atom is seven coordinated. Study of weak intramolecular Sn?O interactions is very important to decide geometry around tin. Furthermore, it has been investigated that these compounds exhibit fairly good antibacterial, antifungal, cytotoxic, insecticidal and antiurease activities.     

Synthesis and characterization of Ru(arene) complexes of bispyrazolylazines: Catalytic hydrogen transfer of ketones

The bis(pyrazol-1-yl)azine ligands 2,3-bis(pyrazol-1-yl)quinoxaline (bpzqnx), 2,3-bis(pyrazol-1-yl)pyrazine (bpzprz) and 3,6-bis(3,5-dimethylpyrazol-1-yl)pyridazine (bpz*pdz) were prepared by the reaction of pyrazolate salts and the corresponding azine dichloride derivatives. The reaction of these ligands with Ru(arene) precursors led to the mononuclear complexes [RuCl(arene)(L)]BPh₄ (arene = p-cymene, L = bpzqnx, 1, bpzprz, 5, bpz*pdz, 7; arene = C₆H₆, L = bpzqnx, 2, bpzprz, 6, bpz*pdz, 8) with the N-donor ligand coordinated in a bidentate chelate way. In general, the ligands coordinate through one pyrazole ring and the azine, except in the cases of 1 and 2 where the two pyrazolyl rings are coordinated to the metal in a symmetrical way. When the reactions between the ruthenium precursors and bpzqnx are carried out in MeOH, the complexes [RuCl(arene)(OMepzqnx)]BPh₄ with partially methanolyzed ligands are isolated (arene = p-cymene, 3; C₆H₆, 4). In this process a methoxy group has replaced one of the pyrazole groups in the ligand. The X-ray structures of 6 and 7 have been determined. These compounds have a three-legged piano-stool structure with cations and anions packed through weak interactions. Complexes 1-8 are active in ketone hydrogenation transfer processes even in the absence of base.     

Search for multifunctional agents against Alzheimer’s disease among non-imidazole histamine H3 receptor ligands. In vitro and in vivo pharmacological evaluation and computational studies of piperazine derivatives

In the search for new treatments for complex disorders such as Alzheimer’s disease the Multi-Target-Directed Ligands represent a very promising approach. The aim of the present study was to identify multifunctional compounds among several series of non-imidazole histamine H3 receptor ligands, derivatives of 1-[2-thiazol-5-yl-(2-aminoethyl)]-4-n-propylpiperazine, 1-[2-thiazol-4-yl-(2-aminoethyl)]-4-n-propylpiperazine and 1-phenoxyalkyl-4-(amino)alkylopiperazine using in vitro and in vivo pharmacological evaluation and computational studies. Performed in vitro assays showed moderate potency of tested compounds against acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). Molecular modeling studies have revealed possible interactions between the active compounds and both AChE and BuChE as well as the human H3 histamine receptor. Computational studies showed the high drug-likeness of selected compounds with very good physicochemical profiles. The parallel artificial membrane permeation assay proved outstanding blood–brain barrier penetration in test conditions. The most promising compound, A12, chemically methyl(4-phenylbutyl){2-[2-(4-propylpiperazin-1-yl)-1,3-thiazol-5-yl]ethyl}amine, possesses good balanced multifunctional profile with potency toward studied targets - H3 antagonist activity (pA₂ = 8.27), inhibitory activity against both AChE (IC₅₀ = 13.96 μM), and BuChE (IC₅₀ = 14.62 μM). The in vivo pharmacological studies revealed the anti-amnestic properties of compound A12 in the passive avoidance test on mice.     

Intercalative DNA Binding of Model Compounds Derived From Metabolites of 7, 12-Dimethylbenz[a]anthracene

Abstract

The DNA binding of nonreactive model compounds of metabolites of 7,12-dimethylbenz[a]-anthracene (DMBA)¹ was studied in fluorescence quenching and fluorescence lifetime experiments. The model compounds examined were DMA and 8,9,10,11-tetrahydro-BA. DMA is a π electron model of a highly carcinogenic bay region epoxide of DMBA. 8,9,10,11- tetrahydro-BA is a model compound of a less carcinogenic DMBA epoxide.

The results indicate that the binding of DMA occurs primarily via intercalation. In 15% methanol the binding constant is 3.1 × 10³M^?1. In 15% methanol and at DNA phosphate levels of 5.0 × ^?4 M the intercalative binding of DMA is reduced by a factor of 6.2 when 5.0 × 10^?4 M Mg⁺² is added. The DMA binding constant for intercalation is reduced by more than a factor of 4 when the methanol content of the solvent is increased from 0% to 20%. Finally DMA binding arising from π interactions with the DNA bases is reduced more than 15 times when the DNA is denatured. For 8,9,10,11-tetrahydro-BA in 15% methanol the binding constant for intercalation is 6 times lower than that for DMA.

These results along with previously reported binding data on other model compounds suggest that bay region metabolites of DMBA readily participate in physical π stacking interactions with DNA.     

Ultrasound mediated efficient synthesis of new 4-oxoquinazolin-3(4H)-yl)furan-2-carboxamides as potent tyrosinase inhibitors: Mechanistic approach through chemoinformatics and molecular docking studies

We have carried out the synthesis of new 4-oxoquinazolin-3(4H)-yl)furan-2-carboxamide derivatives by the reaction between isatoic anhydride, 2-furoic hydrazide and substituted salicylaldehydes in ethanol: water (5:5 v/v) solvent system using p-TSA as a catalyst under ultrasound irradiation at room temperature. The structures of newly synthesized compounds were confirmed through spectral techniques such as IR, ¹H NMR, ¹³C NMR, and LCMS. The important features of this protocol include simple and easy workup procedure, reaction carried out at ambient temperature, use of ultrasound and high yield of oxoquinazolin-3(4H)-yl)furan-2-carboxamides in short reaction time. The synthesized compounds 4a–4j were screened against tyrosinase enzyme and all these compounds found to be potent inhibitors with much lower IC₅₀ value of 0.028 ± 0.016 to 1.775 ± 0.947 µM than the standard kojic acid (16.832 ± 1.162 µM). The kinetics mechanism for compound 4e was analyzed by Lineweaver-Burk plots which revealed that compound inhibited tyrosinase non-competitively by forming an enzyme-inhibitor complex. Along with this all the synthesized compounds (4a–4j) were scanned for their DPPH free radical scavenging ability. The outputs received through in vitro and in silico analysis are coherent to the each other with good binding energy values (kcal/mol) posed by synthesized ligands.     

Nickel-quinolones interaction: Part 3 — Nickel(II) complexes of the antibacterial drug flumequine

Nickel(II) complexes with the first-generation quinolone antibacterial agent flumequine in the presence or absence of nitrogen donor heterocyclic ligands (4-benzylpyridine, pyridine, 2,2′-bipyridine or 1,10-phenanthroline) have been structurally characterized by physicochemical and spectroscopic techniques. The experimental data suggest that flumequine acts as deprotonated bidentate ligand coordinated to Ni(II) through the carboxylato and ketone oxygen atoms. The crystal structures of bis(4-benzylpyridine)bis(flumequinato)nickel(II) 2, (2,2′-bipyridine)bis(flumequinato)nickel(II) 4 and (1,10-phenanthroline)bis(flumequinato)nickel(II) 5 have been determined by X-ray crystallography and are the first crystal structures of flumequinato complexes reported. UV study of the interaction of the complexes with calf-thymus DNA (CT DNA) has shown that the complexes bind to CT DNA and bis(aqua)bis(flumequinato)nickel(II) exhibits the highest binding constant to CT DNA. Competitive study with ethidium bromide (EB) has shown that the complexes can displace the DNA-bound EB indicating that they bind to DNA in strong competition with EB. The cyclic voltammograms of the complexes recorded in DMSO solution and in 1/2 DMSO/buffer (containing 150 mM NaCl and 15 mM trisodium citrate at pH 7.0) solution have shown that in the presence of CT DNA they bind to CT DNA by the intercalative binding mode. The complexes exhibit good binding propensity to human or bovine serum albumin protein having relatively high binding constant values.     

Potent mGluR5 antagonists: pyridyl and thiazolyl-ethynyl-3,5-disubstituted-phenyl series

We report the synthesis of four series of 3,5-disubstituted-phenyl ligands targeting the metabotropic glutamate receptor subtype 5: (2-methylthiazol-4-yl)ethynyl (1a-j,), (6-methylpyridin-2-yl)ethynyl (2a-j), (5-methylpyridin-2-yl)ethynyl (3a-j,), and (pyridin-2-yl)ethynyl (4a-j,). The compounds were evaluated for antagonism of glutamate-mediated mobilization of internal calcium in an mGluR5 in vitro assay. All compounds were found to be full antagonists and exhibited low nanomolar to subnanomolar activity.     

The effect of pyridyl substituents on the thermodynamics of porphyrin binding to G-quadruplex DNA

Most of the G-quadruplex interactive molecules reported to date contain extended aromatic flat ring systems and are believed to bind principally by π–π stacking on the end G-tetrads of the quadruplex structure. One such molecule, TMPyP4, (5,10,15,20-tetra(N-methyl-4-pyridyl)porphyrin), exhibits high affinity and some selectivity for G-quadruplex DNA over duplex DNA. Although not a realistic drug candidate, TMPyP4 is used in many nucleic acid research laboratories as a model ligand for the study of small molecule G-quadruplex interactions. Here we report on the synthesis and G-quadruplex interactions of four new cationic porphyrin ligands having only 1, 2, or 3 (N-methyl-4-pyridyl) substituents. The four new ligands are: P(5) (5-(N-methyl-4-pyridyl)porphyrin), P(5,10) (5,10-di(N-methyl-4-pyridyl)porphyrin), P(5,15) (5,15-di(N-methyl-4-pyridyl)porphyrin), and P(5,10,15) (5,10,15-tri(N-methyl-4-pyridyl)porphyrin). Even though these compounds have been previously synthesized, we report alternative synthetic routes that are more efficient and that result in higher yields. We have used ITC, CD, and ESI-MS to explore the effects of the number of N-methyl-4-pyridyl substituents and the substituent position on the porphyrin on the G-quadruplex binding energetics. The relative affinities for binding these ligands to the WT Bcl-2 promoter sequence G-quadruplex are: K_TMPyP4 ≈ K_P(5,15) > K_P(5,10,15) >>> K_P(5,10), K_P(5). The saturation stoichiometry is 2:1 for both P(5,15) and P(5,10,15), while neither P(5) nor P(5,10) exhibit significant complex formation with the WT Bcl-2 promoter sequence G-quadruplex. Additionally, binding of P(5,15) appears to interact by an ‘intercalation mode’ while P(5,10,15) appears to interact by an ‘end-stacking mode’.     

Iodine catalyzed three component synthesis of 1-((2-hydroxy naphthalen-1-yl)(phenyl)(methyl))pyrrolidin-2-one derivatives: Rationale as potent PI3K inhibitors and anticancer agents

A series of 1-((2-hydroxynaphthalen-1-yl)(phenyl)(methyl))pyrrolidin-2-one derivatives by an efficient iodine catalyzed domino reaction involving various aromatic aldehydes, 2-pyrrolidinone and β-naphthol was achieved and the structures were elucidated by FTIR ¹H NMR, ¹³C NMR, and HRMS. Subsequently they were evaluated for cytotoxicity against breast cancer (MCF-7), colon cancer (HCT116) cell lines. In the cytotoxicity, the relative inhibition activity was remarkably found to be high in MCF-7 cell lines as 79% (4c), 83% (4f) and the IC₅₀values were 1.03 µM (4c), 0.98 µM (4f). Compounds 4a, 4e, 4k–m, and 4q were found to be inactive and rest showed a moderate activity. In order to get more insight into the binding mode and inhibitor binding affinity, compounds (4a–q) were docked into the active site phosphoinositide 3-kinase (PI3K) (PDB ID: 4JPS) which is a crucial regulator of apoptosis or programmed cell death. Results suggested that the hydrophobic interactions in the binding pockets of PI3K exploited affinity of the most favourable binding ligands (4c and 4f: inhibitory constant (ki) = 66.22 nM and 107.39 nM). The SAR studies demonstrated that the most potent compounds are 4c and 4f and can be developed into precise PI3K inhibitors with the capability to treat various cancers.     

Synthesis and DNA interaction of ethylenediamine platinum(II) complexes linked to DNA intercalants

A series of ethylenediamine platinum(II) complexes connected through semi-rigid chains of 1,2-bis(4-pyridyl)ethane to DNA intercalating subunits (naphthalene, anthracene or phenazine) has been synthesized, and their interactions with calf thymus (CT) DNA have been evaluated by viscometric titrations and equilibrium dialysis experiments. The parent ligands that contain anthracene or phenazine chromophores showed a monointercalative mode of DNA interaction (especially the anthracene derivative), with apparent association constants in the order of 10⁴ M^?1. The corresponding platinum(II) complexes bind CT DNA through bisintercalation, as established by the significant increase of DNA contour length inferred from viscosity measurements, and the association constants are in the order of 10⁵ M^?1. The naphthalene derivatives, however, exhibit a mixed mode of interaction, which suggests a partial contribution of both intercalation and groove binding for the ligand, and monointercalation in the case of the platinum(II) complex. Competition dialysis experiments carried out on the intercalative compounds have revealed a moderate selectivity towards GC DNA sequences for the derivatives containing the anthracene chromophore.     

New pyrazoline bearing 4(3H)-quinazolinone inhibitors of monoamine oxidase: Synthesis,biological evaluation,and structural determinants of MAO-A and MAO-B selectivity

A new series of pyrazoline derivatives were prepared starting from a quinazolinone ring and evaluated for antidepressant, anxiogenic and MAO-A and -B inhibitory activities by in vivo and in vitro tests, respectively. Most of the synthesized compounds showed high activity against both the MAO-A (compounds 4a–4h, 4j–4n, and 5g–5l) and the MAO-B (compounds 4i and 5a–5f) isoforms. However, none of the novel compounds showed antidepressant activity except for 4b. The reason for such biological properties was investigated by computational methods using recently published crystallographic models of MAO-A and MAO-B. The differences in the intermolecular hydrophobic and H-bonding of ligands to the active site of each MAO isoform were correlated to their biological data. Compounds 4i, 4k, 5e, 5i, and 5l were chosen for their ability to reversibly inhibit MAO-B and MAO-A and the availability of experimental inhibition data. Observation of the docked positions of these ligands revealed interactions with many residues previously reported to have an effect on the inhibition of the enzyme. Among the pyrazoline derivatives, it appears that the binding interactions for this class of compounds are mostly hydrophobic. All have potential edge-to-face hydrophobic interactions with F343, as well as π–π stacking with Y398 and other hydrophobic interactions with L171. Strong hydrophobic and H-bonding interactions in the MAO recognition of 4i could be the reason why this compound shows selectivity toward the MAO-B isoform. The very high MAO-B selectivity for 4i can be also explained in terms of the distance between the FAD and the compound, which was greater in the complex of MAO-A-4i as compared to the corresponding MAO-B complex.     

Design and synthesis of aminoester heterodimers containing flavone or chromone moieties as modulators of P-glycoprotein-based multidrug resistance (MDR)

In this study, a new series of heterodimers was synthesized. These derivatives are N,N-bis(alkanol)amine aryl esters or N,N-bis(ethoxyethanol)amine aryl esters carrying a methoxylated aryl residue combined with a flavone or chromone moiety. The new compounds were studied to evaluate their P-gp modulating activity on a multidrug-resistant leukemia cell line. Some of the new compounds show a good MDR reversing activity; interestingly this new series of compounds does not comply with the structure-activity relationships (SAR) outlined by previously synthesized analogs carrying different aromatic moieties. In the case of the compounds described in this paper, activity is linked to different features, in particular the characteristics of the spacer, which seem to be critical for the interaction with the pump. This fact indicates that the presence of a flavone or chromone residue influences the SAR of these series of products, and that flexible molecules can find different productive binding modes with the P-gp recognition site. These results support the synthesis of new compounds that might be useful leads for the development of drugs to control P-gp-dependent MDR.     

Rational design,synthesis, pharmacophore modeling,and docking studies for identification of novel potent DNA-PK inhibitors

Drugs of cancer based upon ionizing radiation or chemotherapeutic treatment may affect breaking of DNA double strand in cell. DNA-PK enzyme has emerged as an attractive target for drug discovery efforts toward DNA repair pathways. Hence, the search for potent and selective DNA-PK inhibitors has particularly considered state-of-the art and several series of inhibitors have been designed. In this article, a novel benchmark DNA-PK database of 43 compounds was built and described. Ligand-based approaches including pharmacophore and QSAR modeling were applied and novel models were introduced and analyzed for predicting activity test for DNA-PK drug candidates. Based upon the modeling results, we gave a report of synthesis of fifteen novel 2-((8-methyl-2-morpholino-4-oxo-4H-benzo[e][1,3]oxazin-7-yl)oxy)acetamide derivatives and in vitro evaluation for DNA-PK inhibitory and antiproliferative activities. These fifteen compounds overall are satisfied with Lipinski's rule of five. The biological testing of target compounds showed five promising active compounds 7c, 7d, 7f, 9e and 9f with micromolar DNA-PK activity range from 0.25 to 5 µM. In addition, SAR of the compounds activity was investigated and confirmed that the terminal aryl moiety was found to be quite crucial for DNA-PK activity. Moreover flexible docking simulation was done for the potent compounds into the putative binding site of the 3D homology model of DNA-PK enzyme and the probable interaction model between DNA-PK and the ligands was investigated and interpreted.     

Cytotoxicity and topoisomerase I/II inhibition of glycosylated 2-phenyl-indoles, 2-phenyl-benzo[b]thiophenes and 2-phenyl-benzo[b]furans

A panel of glycosylated DNA binding agents (1-12) designed as functional anthracycline mimics was screened against three solid-tumor cell lines (MCF-7, HT 29 and HepG2/C3A) and three non-tumor cell lines by the MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) cell viability assay. Several compounds showed better in vitro cytotoxicity and selectivity against MCF-7 cells than daunomycin and doxorubicin, two known DNA binding agents that are clinically-used anti-cancer agents. Although the selectivity for HT 29 and HepG2/C3A cells is generally lower, the IC₅₀ values of some analogs against these two cancer cell lines were of the same magnitude as doxorubicin. Because there was no correlation between DNA binding affinity and cytotoxicity, and because topoisomerase (Topo) inhibition is another biological mechanism of action of most anthracycline drugs, Topo I/II inhibition assays with 1-12 were performed. Some of the compounds showed strong inhibition against these enzymes at 100 ??M, but there was no clear correlation between cytotoxicity and Topo I/II inhibition ability. Topo I/II inhibition mode assays were also performed, which verified that these compounds are topoisomerase suppressors, not poisons. Based on these results, we conclude that although DNA binding and/or topoisomerase inhibition may contribute to the observed cytotoxicity of 1-12, other mechanisms of action are also likely to be important.