Design, synthesis, and molecular docking study of novel quinoline-based bis-chalcones as potential antitumor agents.

A novel series of quinoline-based symmetrical and unsymmetrical bis-chalcones was synthesized via a Claisen-Schmidt condensation reaction between 3-formyl-quinoline/quinolone derivatives with acetone or arylidene acetones, respectively, by using KOH/MeOH/H2 O as a reaction medium. Twelve of the obtained compounds were evaluated for their in vitro cytotoxic activity against 60 different human cancer cell lines according to the National Cancer Institute protocol. Among the screened compounds, the symmetrical N-butyl bis-quinolinyl-chalcone 14g and the unsymmetrical quinolinyl-bis-chalcone 17o bearing a 7-chloro-substitution on the N-benzylquinoline moiety and 4-hydroxy-3-methoxy substituent on the phenyl ring, respectively, exhibited the highest overall cytotoxicity against the evaluated cell lines with a GI50 range of 0.16-5.45 µM, with HCT-116 (GI50 = 0.16) and HT29 (GI50 = 0.42 µM) (colon cancer) representing best-case scenarios. Notably, several GI50 values for these compounds were lower than those of the reference drugs doxorubicin and 5-FU. Docking studies performed on selected derivatives yielded very good binding energies in the active site of proteins that participate in key carcinogenic pathways.

Alkaline Phosphatases: in Silico Study on the Catalytic Effect of Conserved Active Site Residues Using Human Placental Alkaline Phosphatase (PLAP) As a Model Protein.

The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.

Curcumin Conjugates of Non-steroidal Anti-Inflammatory Drugs: Synthesis, Structures, Anti-proliferative Assays, Computational Docking, and Inflammatory Response.

In an effort to combine the anti-proliferative effect of CUR-BF2 and CUR compounds with anti-inflammatory benefits of non-steroidal anti-inflammatory drugs (NSAIDs), a library of the bis- and mono-NSAID/CUR-BF2 and NSAID/CUR conjugates were synthesized by coupling flufenamic acid, flurbiprofen, naproxen, indomethacin, and ibuprofen to diversely substituted hydroxy-benzaldehydes via an ester linkage, and by subsequent reaction with acetylacetone-BF2 to form the bis- and the mono-NSAID/CUR-BF2 adducts. Since conversion to NSAID/CUR by the previously developed decomplexation protocol showed limited success, a set of NSAID/CUR conjugates were independently prepared by directly coupling the NSAIDs with parent curcumin. The bis-NSAID/CUR-BF2 and bis-NSAID-CUR hybrids exhibited low cytotoxicity in NCI-60 assay, and in independent cell viability assay on colorectal cancer (CRC) cells (HCT116, HT29, DLD-1, RKO, SW837, CaCo2) and in normal CR cells (CCD841CoN). By contrast, the mono-naproxin and mono-flurbiprofen CUR-BF2 adducts exhibited remarkable anti-proliferative and apoptopic activity in NCI-60 assay most notably against HCT-116 (colon), OVCAR-3 (ovarian), and ACHN (renal) cells. Computational molecular docking calculations showed favorable binding energies to HER2, VEGFR2, BRAF, and Bcl-2 as well as to COX-1 and COX-2, which in several cases exceeded known inhibitors. The main interactions between the ligands and the proteins were hydrophobic, although several hydrogen bonds were also observed. A sub-set of six compounds that had exhibited little or no cytotoxicity were tested for their anti-inflammatory response with THP-1 human macrophages in comparison to parent NSAIDs or parent curcumin.

Recent Advances in the Development of "Curcumin Inspired" Compounds as New Therapeutic Agents.

Despite a huge body of research in the past two decades investigating the antioxidant, antiinflammatory, anti-microbial, and anti-carcinogenic properties of curcumin (CUR), a CUR-based antitumor drug is yet to be developed. Lack of success in achieving this goal stems from CUR's unfavorable biophysicochemical features, particularly poor solubility, low bioavailability, and rapid metabolism, coupled with a complex biological profile making it difficult to determine its mechanism of action. A significant body of literature aimed at improving its physicochemical properties through synthesis or by designing delivery methods has been published, and the progress in these areas has been reviewed. The present review aims to summarize recent progress in the synthesis of structurally diverse "curcumin-inspired" compounds along with computational docking and bioassay studies, through which a number of promising analogs have been identified that warrant further study.

Catalyst-free assembly of giant tris(heteroaryl)methanes: synthesis of novel pharmacophoric triads and model sterically crowded tris(heteroaryl/aryl)methyl cation salts.

A series of giant tris(heteroaryl)methanes are easily assembled by one-pot three-component synthesis by simple reflux in ethanol without catalyst or additives. Diversely substituted indoles (Ar1) react with quinoline aldehydes, quinolone aldehydes, chromone aldehydes, and fluorene aldehydes (Ar2CHO) and coumarins (Ar3) in 1:1:1 ratio to form the corresponding tris(heteroaryl)methanes (Ar1Ar2Ar3)CH along with (Ar1Ar1Ar2)CH triads. A series of new 2:1 triads were also synthesized by coupling substituted indoles with Ar2CHO. The coupling reactions could also be carried out in water (at circa 80 °C) but with chemoselectivity favoring (Ar1Ar1Ar2)CH over (Ar1Ar2Ar3)CH. The molecular structure of a representative (Ar1Ar2Ar3)CH triad was confirmed by X-ray analysis. Model tris(heteroaryl/aryl)methylium salts were generated by reaction with DDQ/HPF6 and studied by NMR and by DFT and GIAO-DFT.

Deuterated Curcuminoids: Synthesis, Structures, Computational/Docking and Comparative Cell Viability Assays against Colorectal Cancer.

A series of deuterated curcuminoids (CUR) were synthesized, bearing two to six OCD3 groups, in some cases in combination with methoxy groups, and in others together with fluorine or chlorine atoms. A model ring-deuterated hexamethoxy-CUR-BF2 and its corresponding CUR compound were also synthesized from a 2,4,6-trimethoxybenzaldehyde-3,5-d2 precursor. As with their protio analogues, the deuterated compounds were found to remain exclusively in the enolic form. The antiproliferative activities of these compounds were studied by in vitro bioassays against a panel of 60 cancer cell lines, and more specifically in human colorectal cancer (CRC) cells (HCT116, HT29, DLD-1, RKO, SW837, and Caco2) and in normal colon cells (CCD841CoN). The deuterated CUR-BF2 adducts exhibited better overall growth inhibition by NCI-60 assay, while for other CUR-BF2 adducts the non-deuterated analogues were more cytotoxic. Results of the more focused comparative cell viability assays followed the same trend, but with some variation depending on cell lines. The CUR-BF2 adducts exhibited significantly higher cytotoxicity than CURs. Structural studies (X-ray and DFT) and computational molecular docking calculations comparing their inhibitory efficacy with those of known anticancer agents used in chemotherapy are also reported.

Synthesis, Computational Docking Study, and Biological Evaluation of a Library of Heterocyclic Curcuminoids with Remarkable Antitumor Activity.

In a continuing search for curcuminoid (CUR) compounds with antitumor activity, a novel series of heterocyclic CUR-BF2 adducts and CUR compounds based on indole, benzothiophene, and benzofuran along with their aryl pyrazoles were synthesized. Computational docking studies were performed to compare binding efficiency to target proteins involved in specific cancers, namely HER2, proteasome, VEGFR, BRAF, and Bcl-2, versus known inhibitor drugs. The majority presented very good binding affinities, similar to, and even more favorable than those of known inhibitors. The indole-based CUR-BF2 and CUR compounds and their bis-thiocyanato derivatives exhibited high anti-proliferative and apoptotic activity by in vitro bioassays against a panel of 60 cancer cell lines, more specifically against multiple myeloma (MM) cell lines (KMS11, MM1.S, and RPMI-8226) with significantly lower IC50 values versus healthy PBMC cells; they also exhibited higher anti-proliferative activity in human colorectal cancer cells (HCT116, HT29, DLD-1, RKO, SW837, and Caco2) than the parent curcumin, while showing notably lower cytotoxicity in normal colon cells (CCD112CoN and CCD841CoN).

Quantum-Mechanical Study on the Catalytic Mechanism of Alkaline Phosphatases.

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The catalytic mechanism was examined by quantum-mechanical calculations using an active-site model based on the X-ray crystal structure of the human placental AP. Free energies of activation and of reaction for the catalytic steps were evaluated for a series of aryl and alkyl phosphate esters, and the computational results were compared with experimental values available in the literature. Mechanistic observations previously reported in experimental works were rationalized by the present theoretical study, particularly regarding the difference in the rate-determining step between aryl and alkyl phosphates. The formation rate of the covalent phosphoserine intermediate followed a linear free energy relationship (LFER) with the pKa of the leaving group. This LFER, which could be experimentally determined only for less reactive alkyl phosphates, was verified by the present calculations to apply for the entire set of aryl and alkyl phosphate substrates.

Mutagenicity of heteroaromatic amines: Computational study on the influence of methyl substituents.

Quantum mechanical calculations were performed to elucidate the factors determining the variations in mutagenic activity within groups of isomeric heteroaromatic amines that differ in the position of methyl substituents. Formation energies for noncovalent complexes and covalent DNA adducts were evaluated by means of high level quantum chemical methods. According to the computational results in this work, covalent adduct stability is proposed to influence the relative mutagenicities of structurally related heterocyclic amines. The stability of covalent C8-dG DNA adducts was found to be mainly determined by π-stacking interactions between the fused ring system of the heteroaromatic amines and the flanking nucleobases. Relative mutagenicity of amines of very related structure is proposed to be regulated by both nitrenium ion and covalent adduct stabilities.

Catalytic activity of human placental alkaline phosphatase (PLAP): insights from a computational study.

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Quantum-mechanical computational methods were employed to study the catalytic mechanism of human placental AP (PLAP). An active-site model was used, constructed on the basis of the X-ray crystal structure of the enzyme. Kinetic and thermodynamic evaluations were achieved for each reaction step. Calculations shed light on the mechanistic differences that had been experimentally observed between aryl and alkyl phosphates, particularly regarding the rate-determining step. The functional implications of relevant residues in the active site were examined. The present theoretical study rationalizes experimental observations previously reported in the literature.

Quantum-chemical studies on mutagenicity of aromatic and heteroaromatic amines.

Arylamines are well-known as widespread industrial and environmental mutagens and carcinogens. Their bioactivity stems from enzymatic metabolic activation to reactive and highly electrophilic intermediates. In this work, computational investigations related to the biological activity of these compounds have been reviewed, especially focusing on studies reporting results from quantum-mechanical calculations. Correlations between relative mutagenicities and structural and electronic features of the parent amines and of their derived nitrenium ion intermediates were examined, with the aim of achieving a clearer comprehension of the main factors determining the genotoxic potential of this type of compounds.

Experimental and GIAO 15N NMR study of substituent effects in 1H-tetrazoles.

A series of 1-aryl/alkyl-1H-1,2,3,4-tetrazoles, 5-substituted 1H-tetrazoles, and 1,5- and 2,5-disubstituted 1H-tetrazoles were studied by a combination of experimental NMR (natural abundance (15)N, (15)N/(1)H HMBC, and (13)C) and computational GIAO-NMR techniques to explore substituent effects on (15)N (and (13)C) NMR chemical shifts in the tetrazole (TA) moiety. Computed (15)N chemical shifts via GIAO-B3LYP/6-311+G(2d,p) calculations gave satisfactory results in comparison with experimental data. Whereas N-alkylation leads to large (15)N chemical shift changes, changes in the N(1)-aryl derivatives bearing diverse substituent(s) are generally small except for polar ortho-substituents (COOH, NO(2)). Large Δδ(15)N values were computed in N(1)-aryl derivatives for p-COH(2)(+) and p-OMeH(+) as extreme examples of electron-withdrawing substituents on a TA moiety.

Computational modeling of the catalytic mechanism of human placental alkaline phosphatase (PLAP).

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Quantum mechanical, molecular dynamics, and molecular docking techniques were applied to computationally model the catalytic mechanism of human placental AP (PLAP). Kinetic and thermodynamic evaluations were performed for each reaction step. The functional significances of the more important residues within the active site were analyzed. The role of the metal ion at the metal binding site M3 was also examined. The calculated activation and reaction energy and free energy values obtained suggested the nucleophilic attack of the Ser92 alkoxide on the phosphorus atom of the substrate would be the rate-limiting step of the catalytic hydrolysis of alkyl phosphate monoesters by PLAP. The reactivities of the wild-type M3-Mg enzyme and the M3-Zn protein were compared, and the main difference observed was a change in the coordination number of the M3 metal for the M3-Zn enzyme. This modification in the active site structure lowered the free energy profile for the second chemical step of the catalytic mechanism (hydrolysis of the covalent phosphoserine intermediate). Consequently, a greater stabilization of the phosphoseryl moiety resulted in a small increment in the activation free energy of the phosphoserine hydrolysis reaction. These computational results suggest that the activation of APs by magnesium at the M3 site is caused by the preference of Mg(2+) for octahedral coordination, which structurally stabilizes the active site into a catalytically most active conformation. The present theoretical results are in good agreement with previously reported experimental studies.

Synthesis, trypanocidal activity and molecular modeling studies of 2-alkylaminomethylquinoline derivatives.

Research and development of new drugs effective in the treatment of Trypanosoma cruzi infections are a real need for the 16 million people infected in the Americas. In a previous work, a quinoline derivative substituted by a 2-piperidylmethyl moiety showed to be active against Chagas disease and was considered a lead compound for further optimization. A series of ten analogous derivatives were tested against epimastigotes as a first approach. In view of their promising results, six of them were evaluated against the blood and intracellular replicative forms of the parasite in humans. Among them, compound 12 which possesses a 6-acetamidohexylamino substituent showed remarkable improvement in activity against epimastigotes, trypomastigotes and amastigotes compared with the structure lead, as well as a good selectivity index for the two parasite stages present in humans. In addition, treatment of infected mice with compound 12 induced a significant reduction in parasitemia compared with non-treated mice. Molecular modeling studies were performed by computational methods in order to elucidate the factors determining these experimental bioactivities.

Quantum chemical studies on ultimate carcinogenic metabolites from polycyclic aromatic hydrocarbons.

Polycyclic aromatic hydrocarbons (PAHs) are widespread environmental pollutants well known as mutagenic/carcinogenic agents. This review will discuss recent theoretical studies regarding the stability and reactivity of ultimate carcinogenic metabolites from PAHs, focusing on their diol epoxide and amine derivatives. Geometrical and electronic features will be analyzed in order to obtain structure-activity relationships. Charge delocalization modes (positive charge density distribution), substituent effects, and conformational aspects will be considered. Computed properties will be compared with the available biological activity data. Correlations between experimental mutagenic potencies reported in the literature and calculated reaction energies and electronic properties will be shown. Heteroaromatic compounds (aza-PAHs, thia-PAHs, and heteroaromatic amines) will also be examined. To model the important step of covalent adduct formation, calculation of the adducts resulting from bond formation between some of these electrophilic intermediates and nucleotide bases (guanine, cytosine) will be described.

Carcinogenic carbocyclic and heterocyclic aromatic amines: a DFT study concerning their mutagenic potency.

The relative stability of the nitrenium ions derived from a set of 43 aromatic and heteroaromatic amines of diverse structure was evaluated by density functional theory (DFT) calculations in order to examine the role of these electrophilic intermediates on mutagenic activity. Correlations were sought between calculated properties and mutagenic potencies from the literature. Mutagenicity was found to increase with nitrenium ion stability, which was favored by negative charge development at the exocyclic nitrogen of the ion (q(N)). Distinct correlation functions were observed for the amines grouped according to their classification as aromatic (Ar), heteroaromatic (HAr), imidazocarbocyclic (ImiAr), imidazoheterocyclic (ImiH), dipyridoimidazoles (PI), and quinoxalines (Qx). The influence of the logarithm of the octanol/water partition coefficient (LogP) on the mutagenic potency of the amines selected for this study was also analyzed.

Electrophilic chemistry of thia-PAHs: stable carbocations (NMR and DFT), S-alkylated onium salts, model electrophilic substitutions (nitration and bromination), and mutagenicity assay.

First examples of stable carbocations are reported from several classes of thia-PAHs with four fused rings, namely, benzo[b]naphtho[2,1-d]thiophene (1) and its 3-methoxy derivative (2), phenanthro[4,3-b]thiophene (3) and its 7-methoxy (4), 10-methoxy (5), and 9-methoxy (6) derivatives, phenanthro[3,4-b]thiophene (7) and its 7-methoxy (8) and 9-methoxy (9) derivatives, and 3-methoxybenzo[b]naphtha[1,2-d]thiophene (11). In several cases, the resulting carbocations were also studied by GIAO-DFT. Charge delocalization modes in the resulting carbocations were probed. A series of S-alkylated onium tetrafluoroborates, namely, 1Me+, 1Et+, 2Et+, and 7Me+ (from 1, 2, and 7), 10Me+ and 10Et+ (from benzo[b]naphtha[1,2-d]thiophene 10), 12Me+ and 12Et+ (from phenanthro[3,2-b][1]benzothiophene 12), 13Me+ (from 3-methoxyphenanthro[3,2-b]benzothiophene 13), 14Me+ (from phenanthro[4,3-b][1]benzothiophene 14), and 15Me+ (from 3-methoxyphenanthro[4,3-b][1]benzothiophene 15), were synthesized. PAH-sulfonium salts 1Me+, 1Et+, 10Me+, 10Et+, 12Me+, and 14Me+ proved to be efficient akylating agents toward model nitrogen nucleophile receptors (imidazole and azaindole). Facile transalkylation to model nucleophiles (including guanine) is also supported by favorable reaction energies computed by DFT. Ring opening energies in thia-PAH-epoxides from 1, 3, and 7 and charge delocalization modes in the resulting carbocations were also evaluated. The four-ring-fused thia-PAHs 1, 2, 3, 4, 5, 7, 8, and 11 are effectively nitrated under extremely mild conditions. Nitration regioselectivity corresponds closely to protonation under stable ion conditions. Bromination of 4 and 6 is also reported. Comparative mutagenicity assays (Ames test) were performed on 1 versus 1NO2, 5 versus 5NO2, and 11 versus 11NO2. Compound 5NO2 was found to be a potent direct acting mutagen.

Oxidized metabolites from benzo[a]pyrene, benzo[e]pyrene, and aza-benzo[a]pyrenes. A computational study of their carbocations formed by epoxide ring opening reactions.

A DFT study aimed at understanding structure-reactivity relationships and fluorine substitution effects on carbocation stability in benzo[a]pyrene (BaP), benzo[e]pyrene (BeP), and aza-benzo[a]pyrene (aza-BaP) derivatives are reported. The relative energies of the resulting carbocations are examined and compared, taking into account the available biological activity data on these compounds. O-Protonation of the epoxides and diol epoxides leads to carbocation formation by barrierless processes. Charge delocalization modes in the resulting carbocations were deduced via NPA-derived changes in charges, and fluorine substitution effects were analyzed on the basis of charge density at different carbocation positions. Thus, fluorine substitution at sites bearing negative charge generated inductive destabilization of the carbocation, whereas a fluorine atom at a ring position which presented significant positive charge density produced a less pronounced destabilization due to fluorine p-pi back-bonding. Protonation reactions were also studied for the azaBaPs. In selected cases, the covalent adducts generated via bond formation with the exocyclic nitrogen of cytosine were computed and relative energies and geometries of the resulting adducts were examined.

Ultimate carcinogenic metabolites from aromatic and heterocyclic aromatic amines: a computational study in relation to their mutagenic potency.

The formation of nitrenium ions from their precursors was examined by density functional theory (DFT) calculations in order to analyze the role of these electrophilic intermediates on the mutagenic activity of the parent amines. The relative reactivities for N-O bond dissociation from the N-hydroxy, N-acetoxy and N-sulfate derivatives of aniline were evaluated. Furthermore, the N-acetoxy esters from a set of 17 aromatic and heteroaromatic amines of diverse structure were considered, and correlations were sought between the calculated properties and the reported mutagenic potencies. The mutagenic activity was found to increase when a more negative charge developed at the exocyclic nitrogen of the nitrenium ion (qN) and with nitrenium ion stability. Different functional correlations were observed for the amine derivatives grouped according to their classification as aromatic (Ar), imidazo-carbocyclic (Imi-C), and imidazo-heterocyclic (Imi-H). The formation of N-acetyl nitrenium ions from aromatic amides was also considered and found to be less favorable than nitrenium ion generation from the corresponding amines.

Carbocations from oxidized metabolites of benzo[a]anthracene: a computational study of their methylated and fluorinated derivatives and guanine adducts.

Structure-reactivity relationships and substituent effects on carbocation stability in benzo[a]anthracene (BA) derivatives have been studied computationally at the B3LYP/6-31G and MP2/6-31G levels. Bay-region carbocations are formed by O-protonation of the 1,2-epoxides in barrierless processes. This process is energetically more favored as compared to carbocation generation via zwitterion formation/O-protonation, via single electron oxidation to generate a radical cation, or via benzylic hydroxylation. Relative carbocation stabilities were determined in the gas phase and in water as solvent (PCM method). Charge delocalization mode in the BA carbocation framework was deduced from NPA-derived changes in charges, and substitution by methyl or fluorine was studied at different positions selected on basis of the carbocation charge density. A bay-region methyl group produces structural distortion with consequent deviation from planarity of the aromatic system, which destabilizes the epoxide, favoring ring opening. Whereas fluorine substitution at sites bearing significant positive charge leads to carbocation stabilization by fluorine p-pi back-bonding, a fluorine atom at a ring position which presented negative charge density leads to inductive destabilization. Methylated derivatives are less sensitive to substituent effects as compared to the fluorinated analogues. Although the solvent decreases the exothermicity of the epoxide ring-opening reactions due to greater stabilization of the reactants, it provokes no changes in relative reactivities. Relative energies in the resulting bay-region carbocations are examined taking into account the available biological activity data on these compounds. In selected cases, quenching of bay-region carbocations was investigated by analyzing relative energies (in the gas phase and in water) and geometries of their guanine adducts formed via covalent bond formation with the exocyclic amino group and with the N-7.