An activity prediction model for steroidal and triterpenoidal inhibitors of Acetylcholinesterase enzyme.

Nowadays, the importance of computational methods in the design of therapeutic agents in a more efficient way is indisputable. Particularly, these methods have been important in the design of novel acetylcholinesterase enzyme inhibitors related to Alzheimer's disease. In this sense, in this report a computational model of linear prediction of acetylcholinesterase inhibitory activity of steroids and triterpenes is presented. The model is based in a correlation between binding energies obtained from molecular dynamic simulations (after docking studies) and [Formula: see text] values of a training set. This set includes a family of natural and semi-synthetic structurally related alkaloids reported in bibliography. These types of compounds, with some structural complexity, could be used as building blocks for the synthesis of many important biologically active compounds Therefore, the present study proposes an alternative based on the use of conventional and easily accessible tools to make progress on the rational design of molecules with biological activity.

Combined Experimental and Theoretical Studies on the Radical Nucleophile Addition Reaction for Sulfide- and Selenide-Centered Anions.

The reactivity of sulfur- and selenium-centered nucleophiles toward 1-naphthyl radicals was studied in dimethylsulfoxide. The photostimulated reaction of sulfide anions, -SC(NH)C6H5 (1), -SC(NH)NH2 (2), and -SC(NH)CH3 (3), renders, after the addition of MeI, methyl 1-naphthylsulfide as a main product together with bis(1-naphthyl) sulfide and naphthalene under irradiation. Concordantly, the reaction of selenide anions, -SeC(NH)C6H5 (4), -SeC(NH)NH2 (5), and -SeCN (6), produces methyl 1-naphthyl selenide, bis(1-naphthyl) selenide, and naphthalene in the presence of potassium tert-butoxide anion (entrainment conditions). Absolute rate constants for the coupling of ions 1-6 to 1-naphthyl radicals were determined; as a general trend, the selenide-centered nucleophiles enhance in 2 times the reactivity of their sulfide analogues. From the mechanistic study, it is proposed that the unstable radical anion produced by the addition of the nucleophile to 1-naphthyl radical affords, after fragmentation, 1-naphthylsulfide/selenide anion. In addition, experimental results are discussed in terms of density functional theory calculations. There is a generally good agreement between the experimental and the calculated reactivities, the spin density being the main parameter to describe the difference found among the anions under study. Moreover, the calculations predict that anion -SeC(NH)CH3 (7) would be a good candidate for the synthesis of selenide derivatives.

Photoinduced Synthesis of Dibenzofurans: Intramolecular and Intermolecular Comparative Methodologies.

The SRN1 reaction has been used as a powerful tool for the synthesis of heterocycles, and only a few studies about photoinduced intramolecular cyclization to generate a new C-O bond by a radical pathway have been reported. This work introduces two strategies for the synthesis of substituted dibenzofurans by electron transfer (eT) reactions. The first one is a three-step process that comprises bromination of o-arylphenols, Suzuki-Miyaura cross-coupling and photoinduced cyclization in order to obtain the above-mentioned products. The second one is a metal-free procedure and does not require any photocatalyst. Different solvents were tested, and the yields ranged from low to moderate. A comparison was established between both methodologies, showing that the second one is the most suitable for the synthesis of dibenzofurans.

Photoinduced nucleophilic substitution of iodocubanes with arylthiolate and diphenylphosphanide ions. Experimental and computational approaches.

A new synthetic route to modify the cubane nucleus is reported here. Methyl-4-iodocubane-1-carboxylate (1) and 1,4-diiodocubane (2) were employed as reagents to react with arylthiolate and diphenylphosphanide ions under irradiation in liquid ammonia and dimethylsulphoxide. The reactions proceed to afford thioaryl- and diphenylphosphoryl- cubane derivatives in moderate to good yields. It is also found that the monosubstituted product with retention of the second iodine is an intermediate compound. Mechanistic aspects are supported by DFT calculations.

In search of the best DFT functional for dealing with organic anionic species.

Quantum chemical computational methods are thought to have problems in dealing with unstable organic anions. This work assesses the ability of different Density Functional Theory (DFT) functionals to reproduce the electron affinity and reduction potential of organic compounds. The performance of 23 DFT functionals was evaluated by computing the negative electron affinities (from 0 eV to -3.0 eV) and reduction potentials in acetonitrile (from 0 to -2.7 V). In general, most of the hybrid GGA functionals work fine in the prediction of electron affinities, BPW91, B3PW91 and M06 being the best in each class of functionals (pure, hybrid and meta-GGA functionals, respectively). On the other hand, the ab initio post-Hartree-Fock methods, MP2 and coupled-cluster (CCSD(T)), as well as the double hybrid functionals, B2PLYP and mPW2PLYP, usually fail. For compounds with EAs lower than -1.75 eV, a method for stabilizing the anion, based on solvation with the IEFPCM model, was employed. In this case, BPW91, PBE0 and M06-HF could be the recommended option for the pure, hybrid and meta-GGA functionals, respectively. The situation improves for the evaluation and prediction of redox potentials. In this case the performance of the DFT functionals is better, in part because the solvent assists in the stabilization of the anions. Nevertheless, there is a systematic bias in the calculation of absolute redox potentials, which could be corrected by using a redox partner that helps by the cancellation of errors. In this case, the hybrid and meta-GGA functionals B3PW91, PBE0, TPSSh and M06 are also among the best for computing redox potentials with a mean absolute deviation (MAD) lower than 0.13 V.

Synthesis of Dibenzosultams by "Transition-Metal-Free" Photoinduced Intramolecular Arylation of N-Aryl-2-halobenzenesulfonamides.

A new and general synthetic route to prepare dibenzosultams is here reported. This approach involves the synthesis of N-aryl-2-halobenzenesulfonamides (3), followed by intramolecular C-C photoinduced arylation under soft conditions without the use of "Transition Metal". The photostimulated reactions exhibit very good tolerance to different substituent groups with good to excellent isolated yields (42-98%) of products. Moreover, it is shown that LED (λ = 395 nm) is an efficient light energy source to initiate efficiently the reactions. Theoretical inspection of the mechanism was made to probe the involvement of the radical-anion SRN1 process.

Molecular view of the interaction of S-methyl methanethiosulfonate with DPPC bilayer.

We present molecular dynamics (MD) simulation studies of the interaction of a chemo preventive and protective agent, S-methyl methanethiosulfonate (MMTS), with a model bilayer of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). We analyzed and compared its diffusion mechanisms with the related molecule dimethyl sulfoxide (DMSO). We obtained spatially resolved free energy profiles of MMTS partition into a DPPC bilayer in the liquid-crystalline phase through potential of mean force (PMF) calculations using an umbrella sampling technique. These profiles showed a minimum for MMTS close to the carbonyl region of DPPC. The location of MMTS molecules in the DPPC bilayer observed in the MD was confirmed by previous SERS studies. We decomposed PMF profiles into entropic and enthalpic contributions. These results showed that the driving force for the partitioning of MMTS into the upper region of DPPC is driven by a favorable entropy change while partitioning into the acyl chains is driven by enthalpy. On the other hand, the partition of DMSO into the membrane is not favored, and is driven by entropy instead of enthalpy. Free diffusion MD simulations using all atom and coarse grained (CG) models of DPPC in presence of MMTS were used to analyze the effect of DPPC-MMTS interaction. Density profiles showed that MMTS locates preferentially in the carbonyl region, as expected according to the PMF profile and the experimental evidence. MMTS presented two differential effects over the packing of DPPC hydrocarbonate chains at low or at high molar ratios. An ordering effect was observed when a CG MMTS model was used. Finally, free diffusion MD and PMF decomposition for DMSO were used for comparison.

Solanocapsine derivatives as potential inhibitors of acetylcholinesterase: Synthesis, molecular docking and biological studies.

The investigation of natural products in medicinal chemistry is essential today. In this context, acetylcholinesterase (AChE) inhibitors comprise one type of the compounds most actively studied in the search for an effective treatment of symptoms of Alzheimer's disease. This work describes the isolation of a natural compound, solanocapsine, the preparation of its chemical derivatives, the evaluation of AChE inhibitory activity, and the structure-activity analysis of relevant cases. The influence of structural variations on the inhibitory potency was carefully investigated by modifying different reactive parts of the parent molecule. A theoretical study was also carried out into the binding mode of representative compounds to the enzyme through molecular modeling. The biological properties of the series were investigated. Through this study valuable information was obtained of steroidal alkaloid-type compounds as a starting point for the synthesis of AChE inhibitors.

"Transition-metal-free" synthesis of carbazoles by photostimulated reactions of 2'-halo[1,1'-biphenyl]-2-amines.

An efficient and simple protocol for the preparation of a series of 9H-carbazoles by photostimulated SRN1 substitution reactions is presented. Substituted 9H-carbazoles were synthesized in low to excellent yields (up to 96%) through an intramolecular C­N bond formation of 2'-halo[1,1'-biphenyl]-2-amines by the photoinitiated SRN1 mechanism under mild and "transition-metal-free" conditions. The biphenylamines used as substrates were obtained with isolated yields ranging from 21% to 84% by two approaches: (A) the cross-coupling Suzuki­Miyaura reaction and (B) the radical arylation of anilines. Some key aspects of the proposed mechanism were evaluated at the B3LYP/6-311+G* level.

Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study.

The human multidrug resistance (MDR) P-glycoprotein (P-gp) mediates the extrusion of chemotherapeutic drugs from cancer cells. Modulators are relevant pharmaceutical targets since they are intended to control or to inhibit its pumping activity. In the present work, a common binding site for Rhodamine 123 and modulators with different modulation activity was found by molecular docking over the crystal structure of the mouse P-gp. The modulators involved a family of compounds, including derivatives of propafenone (3-phenylpropiophenone nucleus) and XR9576 (tariquidar). Our results showed that the relative binding energies estimated by molecular docking were in good correlation with the experimental activities. Preliminary classical molecular dynamics results on selected P-gp/modulator complexes were also performed in order to understand the nature of the prevalent molecular interactions and the possible main molecular features that characterize a modulator. Besides, the results obtained with a human P-gp homology model from the mouse structure are also presented and analyzed. Our observations suggest that the hydrophobicity and molecular flexibility are the main features related to the inhibitory activity. The latter factor would increase the modulator ability to fit the aromatic rings inside the transmembrane domain.

Experimental and computational study of 6-exo and 7-endo cyclization of aryl radicals followed by tandem S(RN)1 substitution.

The reaction of N-allyl-N-(2-halobenzyl)-acetamides and derivatives was investigated in liquid ammonia under irradiation with the nucleophiles Me3Sn(-), Ph2P(-) and O2NCH2(-). Following this procedure, novel substituted 2-acetyl-1,2,3,4-tetrahydroisoquinolines and substituted 2-acetyl-2,3,4,5-tetrahydro-1H-benzo[c]azepines were obtained in good yields. These reactions are proposed to occur through the intermediacy of aryl radicals, which by intramolecular 6-exo or 7-endo attack to a double bond cyclize to give aliphatic radicals, which react along the propagation steps of the S(RN)1 chain cycle to afford the cyclic substituted compounds as main products. The reactions were modeled with DFT methods, which provide a rational understanding that relates the product distribution to the structure of the aliphatic radicals proposed as intermediates and the kinetic of their formation.

Nucleophilic substitution of bromonorbornenes and derivatives by electron transfer reactions.

The photoinitiated substitution reactions of anti-7-bromobenzonorbornadiene (5), its syn isomer 6, exo-anti-13-bromobenzocyclobutanorbornene (7), syn-7-bromonorbornene (8) and bromonorbornane (9) with Me(3)Sn(-) and Ph(2)P(-) anions, in liquid ammonia, are here informed to occur with good yields of substitution. The stereochemical outcome is discussed in terms of calculations with the B3LYP functional and the 6-31+G* basis set; the solvent being included as a continuum through the PCM model. The experimental relative chemical reactivity of pairs of substrates toward a given anion is also presented.

Structural characterization of N-methylcarbamate: ß-cyclodextrin complexes by experimental methods and molecular dynamics simulations.

Detailed insights regarding the inclusion process between ß-cyclodextrin and the N-methylcarbamates insecticides like Bendiocarb, Carbaryl, Carbofuran and Promecarb, are proposed in bases of experimental and computational methods. The results from Fourier transform infrared spectroscopy, differential scanning calorimetry, induced circular dichroism and molecular dynamics indicate that only in the case of Promecarb the interaction with the macrocycle is produced by the alkyl rest of the molecule. In all other cases the aromatic moiety is the part of the insecticide that is partially included in the cavity of ß-cyclodextrin.

Interaction of S-methyl methanethiosulfonate with DPPC bilayer.

The present study is a first step towards the investigation of S-methyl methanethiosulfonate (MMTS) interaction with membrane model systems like liposomes. In this paper, the interaction of MMTS with dipalmitoylphosphatidylcholine (DPPC) bilayers was studied by FTIR and SERS spectroscopy. Lysolipid effect on vesicle stability was studied. The results show that MMTS interacts to different extents with the phosphate and carbonyl groups of membranes in the gel and the liquid crystalline states. To gain a deeper insight into MMTS properties that may be potentially helpful in the design of new drugs with therapeutic effects, we performed theoretical studies that may be the basis for the design of their mode of action.

SAR analysis of new dual targeting fluoroquinolones. Implications of the benzenesulfonyl group.

When a benzenesulfonyl moiety (BS) was bound to the N-piperazinyl ring of antibacterial fluoroquinolones (AMFQs) norfloxacin (NOR) or ciprofloxacin (CIP), the resulting benzenesulfonyl-fluoroquinolone (BSFQs) analogs showed an improved in vitro activity against Gram-positive strains. A bioisosterical replacement of the sulfonyl group for a carbonyl group led to the benzenecarboxamide-fluoroquinolones (BCFQs) that showed a similar trend in the antibacterial activity and spectrum. The BSFQs and BCFQs are considered members of the "dual targeting" fluoroquinolones, targeting both DNA gyrase and topoisomerase IV. To disclose the real contribution of the BS/BC moiety in anti-staphylococcal activity, a 3D-QSAR analysis that included calculation of theoretical molecular descriptors and pharmacophore generation was performed. Previous and present QSAR results have confirmed the positive influence on activity of small electron donating p-substituent on the BS or BC moiety. The generated phamacophore model showed that both phenyl and SO2/CO groups are involved in the interaction with receptor. We postulate that the enhanced potency of BSFQs against Staphylococcus aureus compared to CIP and NOR could be caused by the presence of the BS moiety that resulted in enhanced binding to DNA gyrase of Sa. Additionally, their greater ability to enter bacterial cells by diffusion and a reduced susceptibility to FQ-specific efflux pumps could also make a contribution.

Detailed analysis of water structure in a solvent mediated electron tunneling mechanism.

This work aims at describing the water structure characteristics that influence the electron transfer superexchange mechanism by explicitly calculating the solvent mediated conductance between the donor and acceptor in a generic pair. The method employed here is based on the non-equilibrium Green function formalism for calculating the conductance over solvent trajectories previously determined by molecular dynamics methods. A non-exponential dependence of the conductance is observed with respect to the distance between the donor and the acceptor. Local fluctuations of the solvent structure are responsible for the non-monotonic dependence, mainly due to the formation of solvent bridges that act as a molecular wire connecting the sites. This shortcutting phenomenon is observed for certain ranges of distances between the donor and acceptor in the pair. Charge on the sites strongly affects the local solvent structure and causes qualitative changes in the distance dependence of the tunneling probability.

Electron-transfer-mediated synthesis of phenanthridines by intramolecular arylation of anions from N-(ortho-halobenzyl)arylamines: regiochemical and mechanistic analysis.

The synthesis of a series of substituted phenanthridines by photostimulated C-C cyclization of anions from N-(ortho-halobenzyl)arylamines has been found to proceed in very good to excellent yields (79-95%) in liquid ammonia and in DMSO. The N-(ortho-halobenzyl)arylamines are obtained in good to very good isolated yields (44-85%) by nucleophilic substitution of ortho-halobenzylchlorides with different arylamines. The reaction of the anions of a diverse set of N-(ortho-halobenzyl)arylamines was studied, and the methodology was extended to the synthesis of trispheridine, a natural product, in very good yield. In order to explain the regiochemical outcome of these reactions, a theoretical analysis was performed with DFT methods and the B3LYP functional.

Synthesis, stereoelectronic characterization and antiparasitic activity of new 1-benzenesulfonyl-2-methyl-1,2,3,4-tetrahydroquinolines.

The synthesis and full 3D structural characterization of nine new 1-benzenesulfonyl-2-methyl-1,2,3,4-tetrahydroquinoline derivatives are reported. These belong to a library whose rationale for the design was the previous knowledge of the biological relevant properties of both structural moieties. From protozoan antiparasitic screening, compounds 3 demonstrated interesting activity against Trypanozoma cruzi with low cytotoxicity. Besides, most compounds were moderately active against Plasmodium falciparum. Of these, 3 and 9 can be considered as lead scaffolds for further optimization. The substituent on BS did not influence the 3D structure properties and the (1)H NMR spectra revealed the existence of an intramolecular weak hydrogen bond, C-Hcdots, three dots, centeredOS. Molecular modeling and X-ray crystallography also confirmed this finding, which is relevant to compound conformational preference.

In search for an optimal methodology to calculate the valence electron affinities of temporary anions.

Recently, we have proposed an approach for finding the valence anion ground state, based on the stabilization exerted by a polar solvent; the methodology used standard DFT methods and relatively inexpensive basis sets and yielded correct electron affinity (EA) values by gradually decreasing the dielectric constant of the medium. In order to address the overall performance of the new methodology, to find the best conditions for stabilizing the valence state and to evaluate its scope and limitations, we gathered a pool of 60 molecules, 25 of them bearing the conventional valence state as the ground anion and 35 for which the lowest anion state found holds the extra electron in a diffuse orbital around the molecule (non valence state). The results obtained by testing this representative set suggest a very good performance for most species having an experimental EA less negative than -3.0 eV; the correlation at the B3LYP/6-311+G(2df,p) level being y = 1.01x + 0.06, with a correlation index of 0.985. As an alternative, the time dependent DFT (TD-DFT) approach was also tested with both B3LYP and PBE0 functionals. The methodology we proposed shows a comparable or better accuracy with respect to TD-DFT, although the TD-DFT approach with the PBE0 functional is suggested as a suitable estimate for species with the most negative EAs (ca.-2.5 to -3.5 eV), for which stabilization strategies can hardly reach the valence state. As an application, a pool of 8 compounds of key biological interest with EAs which remain unknown or unclear were predicted using the new methodology.

Competitive reaction pathways for o-anilide aryl radicals: 1,5- or 1,6-hydrogen transfer versus nucleophilic coupling reactions. A novel rearrangement to afford an amidyl radical.

The photoinduced reactions of o-iodoanilides (o-IC6H4N(Me)COR, 4a-d) with sulfur nucleophiles such as thiourea anion (1, -SCNH(NH2)), thioacetate anion (2, MeCOS-), and sulfide anion (3, S(2-)) follow different reaction channels, giving the sulfides by a radical nucleophilic substitution or the dehalogenated products by hydrogen atom transfer pathways. After an initial photoinduced electron transfer (PET) from 1 to iodide 4, the o-amide aryl radicals 12 are generated. These aryl radicals 12 afford alternative reaction pathways depending on the structure of the alpha-carbonyl moiety: (a) 12b (R = Me) adds to 1 to render the methylthio-substituted compounds by quenching the thiolate anion intermediate with MeI after irradiation; (b) 12c (R = -CH2Ph) follows a 1,5-hydrogen transfer to give a stabilized alpha-carbonyl radical (17); and (c) 12d (R = t-Bu) affords 1,6-hydrogen transfer, followed by a 1,4-aryl migration to render an amidyl radical (20), which is reduced to the N-benzyl-N,2-dimethylpropanamide (10). Together with this last rearranged product, the ipso substitution derivative was also observed. Similar results were obtained in the PET reactions of 4d (R = t-Bu) with anions 2 and 3 under entrainment conditions with the enolate anion from cyclohexenone (5) or the tert-butoxide anion (6). From this novel rearrangement, and only under reductive conditions by PET reaction with anion 5, iodide 4d (R = t-Bu) affords quantitatively the propanamide 10. The energetic of the intramolecular rearrangements followed by radicals 12b-d were rationalized by B3LYP/6-31+G* calculations.