Medicinal Chemistry - Volume 8, Issue 2, 2012

Magnetic resonance imaging (MRI) is presently the method of choice for detection of brain tumors. However, MRI alone is not conclusive. As the commonly used contrast agents do not bind to the cells and are not taken up into the cells, they generally do accumulate in regions where the blood-brain-barrier is disrupted. While this can be brain tumors (WHO grade II-III and above), it can also be inflammations. A cell-directed contrast agent would be a great asset not only to avoid unnecessary brain biopsies, but also to achieve sharper tumor margins during intraoperative MRI. The gastrin/cholecystockinin receptor found in the brain and the intestinal tract is a potential target for a cell-directed contrast agent. The receptor has already been found in human glioma cell lines and autocrine stimulation has also been demonstrated for the receptor and its ligand gastrin. We coupled the correct and a mutant 17-amino-acid gastrin to gadolinium -1,4,7,10-tetraazacyclododecane-1,4,7,10- tetraacetic acid (an MRI contrast agent) and rhodamine isothiocyanate (a fluorescent dye). Using confocal laser scanning microscopy and magnetic resonance relaxometry experiments we found cytoplasmic uptake of the correct gastrin conjugate into human U373 glioma cells. Surprisingly, the mutant conjugate was also taken up into the cells in a similar pattern, albeit to a lesser degree. Both conjugates showed no cytotoxicity. These conjugates show potential for future use in magnetic resonance imaging studies of brain tumors after systemic or intraoperative local application. The cytoplasm specificity of the conjugates also makes it a potential building block for the design of future cytoplasmdirected imaging and therapeutic conjugates.

Within the United States, primary brain tumors account for 20 to 25 percent of all pediatric cancers. Chemotherapy utilizing a nitrosourea, notably semustine (MeCCNU) and carmustine (BCNU), has shown significant success in the treatment of tumors found in the central nervous system. In silico optimization of molecular properties by substituent substitution that is followed by pattern recognition analysis is utilized in this study to develop 14 novel anti-cancer drugs for the treatment of malignant cancers of the central nervous system. These 14 agents exhibit molecular properties that are suitable for penetration through the blood-brain barrier (BBB). All 14 agents are nitrosoureas having values of Log P ranging from 2.188 to 2.942, and having a constant total of 5 oxygens and nitrogens with zero violations of the Rule of 5 which indicates favorable bioavailability. Value of Log BB (Log [Cbrain/Cblood]) for these agents does not vary from - 0.441 (BB value of 0.362). The formula weight of the agents is highly correlated to molecular volume (r= 0.9848) and total number of atoms (r= 0.9948), but not correlated to number of rotatable bonds (r= 0.1814). Analysis of similarity (ANOSIM) indicated that all 14 new constructs are similar to the parent compound semustine. The Log P value for all 14 agents predicts favorable attributes for penetrating the BBB. Multiple regression analysis established that number of atoms, number of rotatable bonds, and molecular volume are strong prognosticators for molecular weight of this assemblage of pharmaceuticals. This study attests to the efficacy of in silico optimization of molecular substituents followed by pattern recognition analysis to develop new drug designs based on a successful nitrosourea framework for the treatment of malignant tumors of the brain.

As a continuation to our previous work in developing anticancer agents, eighteen symmetrical biphenyl derivatives structurally related to taspine were synthesized and evaluated in vitro and in vivo. All the compounds were prepared with varied substitutions in the phenyl ring of aniline moiety. The cytotoxicity and anticancer activity of biphenyls was evaluated against various human tumor and normal cell line. Antiproliferative assays indicated that some of them exhibited potent anticancer activity. The potent antiproliferative activity of these compounds against ECV304 suggested that these biphenyls could be served as antiangiogenic agents. The highly active compound (2) also exhibited potent growth inhibition against cancer cell lines in vivo. Our findings demonstrated that these symmetrical biphenyl derivatives would be a promising candidate as novel anticancer agents.

Most of cancer chemotherapeutics and chemopreventives exert their effects by triggering apoptotic cell death. In this study, novel benzimidazole and benzothiazole derivatives have been synthesized to investigate their effects on HepG2 liver cancer cell lines after initial screening study. A dose response curve was constructed and the most active derivatives were further studied for apoptotic analysis. Six active benzimidazole derivatives (8, 9, 10, 12, 13 and 14) significantly induced apoptosis compared to control group. Two compounds 10 and 12 induced apoptosis by arresting cells in G1 phase of cell cycle which is confirmed by increased expression level of p21. The activity of caspase-3 which is well known as one of the key executioners of apoptosis was determined in the presence and absence of the tested derivatives. Our results indicated that compounds 10 and 12 significantly increased caspase-3 activity compared to control group. Moreover, a docked pose of compounds 10 and 12 was obtained bound to caspase-3 active site using Molecular Operating Environment module. This study demonstrated that benzimidazole derivatives 10 and 12 provoke cytotoxicity and induced apoptosis in liver cancer cells HepG2.

We have previously found that the dithiocarbamate derivatives of quinazolin-4(3H)-one could act as cytotoxic agents against a panel of human tumor cell lines. To investigate the contribution of dithiocarbamate moiety to the cytotoxic activity, three series of novel quinazolin-4(3H)-one derivatives bearing thiocarbamate, thiourea or Nmethyldithiocarbamate side chains were synthesized and tested for their cytotoxic activity against human cancer cell lines A549, MCF-7, HeLa, HT29 and HCT-116 by MTT assay. The results showed that transformation of the dithiocarbamate moiety in lead compound I to thiocarbamate or thiourea led to a decrease or loss of cytotoxic activity. Some N-alkylated analogs of lead compound II preferentially inhibited the proliferation of A549 cells, although their potencies were not improved in comparison with the unalkylated counterparts. The structure-activity relationship obtained in this research will be beneficial for further synthesis and discovery of effective cytotoxic agents.

Through their reactive oxygen species (ROS) producing function, NADPH oxidase (NOX) enzymes have been linked to several oxidative stress related diseases. In our recently published paper [1] we have already shown the NOX4 inhibitory effect of diverse, molecule sub-libraries and their biological importance. We also presented our work connected to potential anti-tumour molecules and the relationship between their biological activity and physico-chemical properties [2]. As an extension of these studies further physico-chemical and biological investigation has been carried out on a molecule group included NOX4 inhibitory chromanone compounds. Here we describe the optimization of early ADME(T) parameters determining lipophilicity, phospholipophilicity and permeability linked to structure-activity relationship. We prove that optimal lipo- and phospholipophilicty can be also determined in case of NOX4 inhibitors and a comparison will be made between the chemically similar isochromanone and chromanone molecular libraries. It will be also shown how to predict the effect of different substituents on permeability, lipo- and phospholipophilicity and also the biological differences between anti-tumour molecules and NOX4 inhibitors according to their penetration ability.

In an effort to discover new candidates with improved antimicrobial activities, we synthesized and studied invitro antimicrobial activities of various series of 3-((thiophen-2-yl)-ethyl)-2-(styryl)-quinazolin-4(3H)-one (3a-3g) and N1-(substituted aryl)-N3-[3-((3,4-dimethoxy phenyl-2-yl)-ethyl)-4(3H)-quinazolone-2-yl]-acetonyl semicarbazides (7a-7j) with an intent to overcome multiple drug resistance to the pathogenic strains and to retain psychological action to develop novel class of antibacterial agents. The structure of newly synthesized scaffolds has been affirmed on the basis of FTIR, 1H NMR, 13C NMR, mass and elemental analysis. All the final scaffolds have been subjected to in vitro antimicrobial screening against two Gram (+Ve) bacteria (S. aureus, B. subtilis), two Gram (-Ve) bacteria (E. coli, S.typhi) and two fungal strains (C. albicans, A. niger) using the broth micro-dilution method.

Conjugates between suramin, a polyanionic naphthalene sulfonate derivative, and nucleoside reverse transcriptase inhibitors (NRTIs), 3'-azido-2',3'-dideoxythymidine (AZT) and 3'-fluoro-2',3'-dideoxythymidine (FLT), were designed to create an antiretroviral with multiple mechanisms of action that could be developed as an anti-HIV topical microbicide candidate. The anti-HIV activity of these conjugates was compared with that of suramin and the corresponding physical mixtures of suramin and nucleosides. The conjugates were synthesized as sulfonate esters by reaction of suramin with the nucleoside analogs in the presence of phosphorus pentoxide, and were tested against X4 and R5 labadapted strains of HIV-1. Suramin conjugates of AZT (EC50= 19.4 μg/ml) and FLT (EC50= 23.6 μg/ml) demonstrated improved anti-HIV activity against X4 strain of virus by 2.5 and 2 fold, respectively, when compared with suramin. The physical mixtures of suramin with nucleosides significantly improved anti-HIV activity of suramin against X4 strain by more than 55 fold.

Comparative molecular field analysis (CoMFA) is a widely used 3D-QSAR method by which we can investigate the potential relation between biological activity of compounds and their structural features. In this study, a new application of this approach is presented by combining the molecular modeling with a new developed pharmacophore model specific to CYP1A2 active site. During constructing the model, we used the molecular dynamics simulation and molecular docking method to select the sensible binding conformations for 17 CYP1A2 substrates based on the experimental data. Subsequently, the results obtained via the alignment of binding conformations of substrates were projected onto the active- site residues, upon which a simple blueprint of active site was produced. It was validated by the experimental and computational results that the model did exhibit the high degree of rationality and provide useful insights into the substrate binding. It is anticipated that our approach can be extended to investigate the protein-ligand interactions for many other enzyme-catalyzed systems as well.

CYP2E1, as a member of the cytochrome P450s (CYPs) super-family, is in charge of six percent drug metabolism involving a diversity of drugs distinct in structures and chemical properties, such as alcohols, monocyclic compounds (e.g., acetaminophen, benzene, p-nitrophenol), bicyclic heterocycles (e.g., coumarin, caffeine) and even fatty acids. The aromatic molecules form a vital species catalyzed by CYP2E1. To investigate the mechanism of metabolizing a diversity of aromatic molecules, five representative aromatic substrates were selected: (1) benzene, the non-polar simple ring; (2) aniline, the monocyclic substrate with smallest substitution on the phenyl ring; (3) acetaminophen, a large monocyclic substrate with highly active reactivity; (4) chlorzoxazone, and (5) theophylline, the bicyclic substrates with low or high catalytic activities. They were docked into X-ray structure of CYP2E1, after which all-atom molecular dynamics simulations of 5 ns were performed on each model. It was found that the active site interact with the aromatic substrates mainly through π-π stacking, supplied by five hydrophobic phenylalanines in the active site. Our simulations also illustrated the specific movement of different kinds of aromatic substrates in the pocket. Small monocyclic substrates show highly frequent self-rotation and limited translation movement. Substrates with single catalytic position are less movable in the pocket than substrates with multiple products. All these findings are quite useful for understanding the catalytic mechanism of CYP2E1, stimulating novel strategies for conducting further mutagenesis studies for specific drug design.

Arsenic compounds have shown medical usefulness since they proved to be effective in causing complete remission of acute promyelocytic leukemia. In this work we obtained a fluorescently labeled arsenic compound that can be used with current fluorescence techniques for basic and applied research, focused on arsenic-induced apoptosis studies. This compound is an arsanilic acid bearing a covalently linked FITC that was chemically synthesized and characterized by fluorescence, UV-Vis, mass and FTIR spectrometry. In addition, we assessed its apoptotic activity as well as its fluorescent labeling properties in HL60 cell line as a leukemia cell model through flow cytometry. We obtained a compound with a 1:1 FITC:arsenic ratio and a 595 m/z, confirming its structure by FTIR. This compound proved to be useful at inducing apoptosis in the leukemia cell model and labeling this apoptotic cell population, in such a way that the highest FITC fluorescence correlated with the highest arsenic amount.

A comparative analysis of stereo-electronic properties of five cholinesterase reactivators (pralidoxime (2- PAM), trimedoxime, obidoxime, HI-6, and HLo-7) and six “K-oximes” was performed to assess their roles in reactivating OP-inhibited phosphorylated serine residue of mouse AChE. Quantum mechanical (QM) calculations starting from semiempirical to ab initio levels were sequentially performed with hierarchical basis sets to obtain the individual optimized geometry and stereo-electronic properties of the eleven oximes. Next, solvation effects were computed on the optimized structures using two different (PCM and COSMO) QM models. Results indicate that properties, such as the distance between the bisquarternary nitrogen atoms, surface area, molecular volume, and hydrophilicity have important roles in the reactivation of OP-inhibited AChE. Electronic attributes, such as the molecular electrostatic potentials and orbital energies were also found to be important parameters for reactivation. Nucleophilicity of the oxygen atoms at the terminal regions, electrophilicity in the central regions of the oximes, and location of the molecular orbitals on aromatic rings have significant roles for the experimentally observed reactivations in several OP agents inhibited mouse AChE. Analysis of solvation free energy indicates high solute polarization and dispersion energies of the oximes to be particularly critical for the tabun- inhibited mouse AChE, whereas lower values of these properties favor reactivation against other OP agents, such as soman, sarin and cyclosarin. Feature mappings of our recently reported pharmacophore model were also observed to be consistent with the above observed electronic properties. In silico toxicity evaluation on these oximes predicts the Koximes to have somewhat higher oral toxicity compared to the other bispyridinium oximes.

Ketamine (2-o-chlorophenyl-2-methylaminocyclohexan, CAS 1867-66-9, CI-581, Ketalar, I), a potent derivative of Phencyclidine (1-[1-phenylcyclohexyl] piperidine, CAS 956-90-1, PCP, II), and many of its analogues have shown anesthetic and analgesic effects. In this research, new derivatives of I, (2-[p-methoxybenzylamino]-2-[p-methoxyphenyl] cyclohexanone, ket-OCH3, III), (2-[p-methylbenzylamino]-2-[p-methoxyphenyl] cyclohexanone, ket-CH3, IV) and their intermediates (V-VIIII) were synthesized and the acute and chronic pains of III and IV were evaluated on rats using tail immersion (as a model of acute thermal pain) and formalin (as a model of acute and chronic chemical pain) tests. The results werecompared with ketamine and control (saline) groups. The results indicated that in tail immersion and formalin tests, these new derivatives (III and IV) were usually effective for decreasing pain on rats.

Malaria, one of the most widespread and deadly infectious diseases continues to kill over 1 million people every year. This scenario is getting even worse as P. falciparum develops resistance to existing drugs. Thus, there is an imperative need for novel and more effective antimalarials. Farnesyltransferase (PFT) appears to be a promising therapeutic target to development of antimalarial drugs and many analogs of PFT inhibitors have proved active against P. falciparum. In order to shed some light on the structure-activity relationships of 192 tetrahydroquinoline and ethylenediamine derivatives that are active against P.falciparum, exploratory analysis as well as classical and hologram QSAR strategies were employed. No global QSAR could be developed for the whole dataset, instead local QSAR models were developed for 118 compounds (classical QSAR r2=0.78, q2=0.75, r2 pred= 0.77 with 2 PCs; HQSAR r2=0.82, q2=0.72, r2 pred= 0.79 with 3 PCs) and 74 compounds (r2=0.79, q2=0.74, r2 pred= 0.57 with 2PCs; r2=0.86, q2=0.77, r2 pred= 0.75 with 4 PCs) using partial least square (PLS) regression. Furthermore, the careful and integrated analysis of contribution maps and regression vector suggest that these inhibitors might have dissimilar requirements to their biological activity.

A series of hydroxyethylamines has been synthesized from the reaction of (2S,3S )Boc-phenylalanine epoxide with alkyl amines in good yields and evaluated for their in vivo antimalarial activity in mice. Compound 4g presented better activity then the reference artesunate in percentage of inhibition of parasitemia in treated P. berghei-infected mice and compare to the activity of artesunate in the survival of mice 14 days after infection. In addiction, no hemolytic activity was found, which supports that inhibition of parasitemia is due to antimalarial activity. The compound 4g inhibited the differentiation to schizonts suggesting that parasite metabolism is a possible target of 4g. These results indicate that this class of compound possesses promising perspectives for the development of new antimalarial drugs.

Four novel drug designs for the treatment of Mycobacterium tuberculosis are analyzed and shown to prevent the growth and proliferation of this dangerous bacteria. All four agents, designated A, B, C, and D, are hydrazide type compounds, where D has three hydrazide functional groups. Agents B and C have a halogenated aromatic ring substituent, while A contains a pyridine ring. Pharmaceutical properties such as Log P, polar surface area, and violations of the Rule of 5 are determined for all agents. The Polar surface area for these four agents ranged from 55.121 A2 to 165.363 A2 and Log P values for A, B, C, and D were determined at -0.916, 0.95, 0.974, and -4.921, respectively. Drug designs A, B, and C show zero violations of the Rule of 5, where D exhibits only one violation, which are outcomes describing favorable bioavailability. Values of polar surface area for A, B, and C affirm an intestinal absorption of greater than 60% as well as the potential for crossing the blood brain barrier for targeting bacterial meningitis of the central nervous system. Interaction with Mycobacterium tuberculosis was monitored over a 14 day interval with agents at known concentration. Agents A, B, C, and D elicited more than 60% inhibition of bacterial growth by day 14 at concentrations of as little as 30 micrograms/ milliliter. All agents reduced bacteria survival to less than 60% by day 7 of culture. The inhibition of bacterial growth induced by agents A, B, C, and D was comparable to that of isoniazid. K-means cluster analysis of descriptors determined isoniazid most similar to agents A, B, and C. Other characteristics of these small hydrazide compounds render supportive evidence for an efficacious clinical application.

A set of 2-benzylsulfanyl derivatives of benzothiazole was synthesized and evaluated for antimicrobial and cytotoxic activities. The biological screening on antimicrobial activity against a panel of Gram-positive and Gramnegative bacteria, yeasts and fungi identified benzylsulfanyl derivatives of benzothiazole as selective inhibitors of mycobacteria. The lead compounds in the set, dinitro derivatives exhibited significant activity against sensitive and multidrug-resistant strains of M. tuberculosis and low cytotoxicity. The QSAR study indicated that the antituberculotic activity is connected with LUMO and HOMO energies. The lower lipophilicity and the increased size of the molecule contribute to antituberculotic activity. Thus, dinitrobenzylsulfanyl derivatives of benzothiazole represent promising smallmolecule synthetic antimycobacterials. Dedicated to Professor Dr. Karel Waisser on the occasion of his 75th birthday.

Recent studies indicated that andrographolide was a potential antihyperlipidaemic therapeutic agent. In the paper, the synthesis of a series of andrographolide derivatives was described and their antihyperlipidaemic activities were evaluated in vivo. As compared with TG, TC, HDL-C and LDL-C concentrations, some of the derivatives exhibited better antihyperlipidaemic effects than positive control atromide. Therein, compound 6i, which was the most potent compound, could serve as a new lead for further development of antihyperlipidaemic agents.

Anticoagulants are used to prevent the formation and extension of blood clots in various disorders as prophylactic agents for thrombo-embolic disorders. Designing of specific inhibitors against molecular targets that play a pivotal role in the coagulation cascade is indispensable. Clotting Factor Xa is one such attractive target for the design of new oral anticoagulants because of the unique role factor Xa plays in the coagulation cascade as a connection between the extrinsic and intrinsic pathways. Application of computational techniques in drug discovery process helps in identifying parameters which can lead to achieve better pharmacological profile. The docking interactions and QSAR studies performed on series of 4-methy-3-(6-[phenyl methylene] amino} pyridine-3-yl)-2H chromen-2-one derivatives provide significant insights for designing of better ligands as anticoagulants.