Novel betulin derivatives as multidrug reversal agents targeting P-glycoprotein.

Chemotherapy is a powerful means of cancer treatment but its efficacy is compromised by the emergence of multidrug resistance (MDR), mainly linked to the efflux transporter ABCB1/P-glycoprotein (P-gp). Based on the chemical structure of betulin, identified in our previous work as an effective modulator of the P-gp function, a series of analogs were designed, synthesized and evaluated as a source of novel inhibitors. Compounds 6g and 6i inhibited rhodamine 123 efflux in the P-gp overexpressed leukemia cells, K562/Dox, at concentrations of 0.19 µM and 0.39 µM, respectively, and increased the intracellular accumulation of doxorubicin at the submicromolar concentration of 0.098 µM. Compounds 6g and 6i were able to restore the sensitivity of K562/Dox to Dox at 0.024 µM and 0.19 µM, respectively. Structure-activity relationship analysis and molecular modeling revealed important information about the structural features conferring activity. All the active compounds fitted in a specific region involving mainly transmembrane helices (TMH) 4-6 from one homologous half and TMH 7 and 12 from the other, also showing close contacts with TMH 6 and 12. Compounds that bound preferentially to another region were inactive, regardless of their free energy of binding. It should be noted that compounds 6g and 6i were devoid of toxic effects against peripheral blood mononuclear normal cells and erythrocytes. The data obtained indicates that both compounds might be proposed as scaffolds for obtaining promising P-gp inhibitors for overcoming MDR.

The thiophene α-terthienylmethanol isolated from Tagetes minuta inhibits angiogenesis by targeting protein kinase C isozymes α and ß2.

Background: Tumor angiogenesis is considered as a crucial pathologic feature of cancer with a key role in multidrug resistance (MDR). Adverse effects of the currently available drugs and the development of resistance to these remain as the hardest obstacles to defeat. Objetive: This work explores flora from Argentina as a source of new chemical entities with antiangiogenic activity. Methods: Tube formation assay using bovine aortic endothelial cells (BAECs) was the experiment of choice to assess antiangiogenic activity. The effect of the pure compound in cell invasiveness was investigated through the trans-well migration assay. The inhibitory effect of the pure compound on VEGFR-2 and PKC isozymes α and ß2 activation was studied by molecular and massive dynamic simulations. Cytotoxicity on peripheral blood mononuclear cells and erythrocyte cells was evaluated by means of MTT and hemolysis assay, respectively. In silico prediction of pharmacological properties (ADME) and evaluation of drug-likeness features were performed using the SwissADME online tool. Results: Among the plants screened, T. minuta, showed an outstanding effect with an IC50 of 33.6 ± 3.4 µg/ml. Bio-guided isolation yielded the terthiophene α-terthienylmethanol as its active metabolite. This compound inhibited VEGF-induced tube formation with an IC50 of 2.7 ± 0.4 µM and significantly impaired the invasiveness of bovine aortic endothelial cells (BAECs) as well as of the highly aggressive breast cancer cells, MDA-MB-231, when tested at 10 µM. Direct VEGFR-2 and PKC inhibition were both explored by means of massive molecular dynamics simulations. The results obtained validated the inhibitory effect on protein kinase C (PKC) isozymes α and ß2 as the main mechanism underlying its antiangiogenic activity. α-terthienylmethanol showed no evidence of toxicity against peripheral blood mononuclear and erythrocyte cells. Conclusion: These findings support this thiophene as a promising antiangiogenic phytochemical to fight against several types of cancer mainly those with MDR phenotype.

Plant extracts and betulin from Ligaria cuneifolia inhibit P-glycoprotein function in leukemia cells.

Overexpression of P-glycoprotein (P-gp), which is linked to multidrug resistance (MDR), is one of the underlying obstacles to the success of chemotherapy as it reduces the efficacy of anticancer drugs and the side effects of these increase as a result of any increased dose to achieve the therapeutic effect. To identify agents with P-gp inhibitory properties, ethanol extracts from 80 plants were screened for their ability to increase intracellular doxorubicin-associated fluorescence, and the extract of Ligaria cuneifolia was found to be the most effective. Its bioassay-guided isolation yielded the pentacyclic triterpene betulin as active agent. This efficiently inhibited P-gp mediated efflux, as demonstrated by the enhancement of the intracellular accumulation of doxorubicin and rhodamine 123 from 1.56 µM in the P-gp overexpressing MDR leukemia cell, Lucena 1. Betulin was also able to render Lucena 1 sensitive to Dox from 0.39 µM. The docking studies revealed that betulin tightly binds to a key region of the TMDs, with a binding mode overlapping one main site of doxorubicin and, more interestingly, emulating the same contacts as tariquidar, as revealed by the per-residue energetic analysis from molecular dynamics simulations. MTT assay using peripheral blood mononuclear cells and hemolysis assay showed that betulin is devoid of toxicity. These findings provide important evidence that betulin may be a safe and promising entity to be further investigated to develop agents able to overcome P-gp-mediated MDR, resulting in a more effective and less toxic chemotherapy.

Molecular dynamics and structure function analysis show that substrate binding and specificity are major forces in the functional diversification of Eqolisins.

BACKGROUND: Eqolisins are rare acid proteases found in archaea, bacteria and fungi. Certain fungi secrete acids as part of their lifestyle and interestingly these also have many eqolisin paralogs, up to nine paralogs have been recorded. This suggests a process of functional redundancy and diversification has occurred, which was the subject of the research we performed and describe here. RESULTS: We identified eqolisin homologs by means of iterative HMMER analysis of the NR database. The identified sequences were scrutinized for which new hallmarks were identified by molecular dynamics simulations of mutants in highly conserved positions, using the structure of an eqolisin that was crystallized in the presence of a transition state inhibitor. Four conserved glycines were shown to be important for functionality. A substitution of W67F is shown to be accompanied by the L105W substitution. Molecular dynamics shows that the W67 binds to the substrate via a π-π stacking and a salt bridge, the latter being stronger in a virtual W67F/L105W double mutant of the resolved structure of Scytalido-carboxyl peptidase-B (PDB ID: 2IFW). Additional problematic mutations are discussed. Upon sequence scrutiny we obtained a set of 233 sequences that was used to reconstruct a Bayesian phylogenetic tree. We identified 14 putative specificity determining positions (SDPs) of which four are explained by mere structural explanations and nine seem to correspond to functional diversification related with substrate binding and specificity. A first sub-network of SDPs is related to substrate specificity whereas the second sub-network seems to affect the dynamics of three loops that are involved in substrate binding. CONCLUSION: The eqolisins form a small superfamily of acid proteases with nevertheless many paralogs in acidic fungi. Functional redundancy has resulted in diversification related to substrate specificity and substrate binding.

Analogues of the Lignan Pinoresinol as Novel Lead Compounds for P-glycoprotein (P-gp) Inhibitors.

To find novel P-gp-inhibitors, a library of pregnane X receptor (PXR) ligands and the ZINC DrugsNow library were superimposed on the P-gp inhibitor (+)-pinoresinol (1) used as a query for a three-dimensional similarity search. After determining the TanimotoCombo index of similarity with 1, eight compounds from the PXR library and two ZINC compounds were selected for biological evaluation. The P-gp inhibition study showed that compounds 7, 8, and 9 successfully increased intracellular doxorubicin (DOX) accumulation in the P-gp overexpressed Lucena 1 cells from 25, 12.5, and 6.25 µM, respectively. Among a series of analogues of 9, compounds 26-30 were shown to be active, with 26 and 27 causing a significant increase in DOX accumulation from 1.56 µM and rendering Lucena 1 sensitive to DOX from 1.56 and 0.78 µM, respectively. Molecular modeling studies showed that both compounds bind to the P-gp at transmembrane helices (TMH) 4, 5, and 6, with 27 also showing contacts with TMH 3.

Synthesis and preliminary structure-activity relationship study of 2-aryl-2H-pyrazolo[4,3-c]quinolin-3-ones as potential checkpoint kinase 1 (Chk1) inhibitors.

The serine-threonine checkpoint kinase 1 (Chk1) plays a critical role in the cell cycle arrest in response to DNA damage. In the last decade, Chk1 inhibitors have emerged as a novel therapeutic strategy to potentiate the anti-tumour efficacy of cytotoxic chemotherapeutic agents. In the search for new Chk1 inhibitors, a congeneric series of 2-aryl-2 H-pyrazolo[4,3-c]quinolin-3-one (PQ) was evaluated by in-vitro and in-silico approaches for the first time. A total of 30 PQ structures were synthesised in good to excellent yields using conventional or microwave heating, highlighting that 14 of them are new chemical entities. Noteworthy, in this preliminary study two compounds 4e2 and 4h2 have shown a modest but significant reduction in the basal activity of the Chk1 kinase. Starting from these preliminary results, we have designed the second generation of analogous in this class and further studies are in progress in our laboratories.

Mechanism Underlying the Reversal of Drug Resistance in P-Glycoprotein-Expressing Leukemia Cells by Pinoresinol and the Study of a Derivative.

P-glycoprotein (P-gp) is a membrane protein associated with multidrug resistance (MDR) due to its key role in mediating the traffic of chemotherapeutic drugs outside cancer cells, leading to a cellular response that hinders efforts toward successful therapy. With the aim of finding agents that circumvent the MDR phenotype mediated by P-gp, 15 compounds isolated from native and naturalized plants of Argentina were screened. Among these, the non-cytotoxic lignan (±) pinoresinol successfully restored sensitivity to doxorubicin from 7 µM in the P-gp overexpressed human myelogenous leukemia cells, Lucena 1. This resistance-reversing effect was confirmed by competitively increasing the intracellular doxorubicin accumulation and by significantly inhibiting the efflux of doxorubicin and, to a lesser extent, that of rhodamine 123. The activity obtained was similar to that observed with verapamil. No such results were observed in the sensitive parental K562 cell line. To gain deeper insight into the mode of action of pinoresinol, its effect on P-gp function and expression was examined. The docking simulations indicated that the lignan bound to P-gp at the apex of the V-shaped transmembrane cavity, involving transmembrane helices 4, 5, and 6, and partially overlapped the binding region of tariquidar, which was used as a positive control. These results would shed some light on the nature of its interaction with P-gp at molecular level and merit further mechanistic and kinetic studies. In addition, it showed a maximum 29% activation of ATP hydrolysis and antagonized verapamil-stimulated ATPase activity with an IC50 of 20.9 µM. On the other hand, pinoresinol decreased the presence of P-gp in the cell surface. Derivatives of pinoresinol with improved activity were identified by docking studies. The most promising one, the non-cytotoxic 1-acetoxypinoresinol, caused a reversion of doxorubicin resistance from 0.11 µM and thus higher activity than the lead compound. It also caused a significant increase in doxorubicin accumulation. Results were similar to those observed with verapamil. The results obtained positioned these compounds as potential candidates for effective agents to overcome P-gp-mediated MDR, leading to better outcomes for leukemia chemotherapy.

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.

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.

Microbial efflux systems and inhibitors: approaches to drug discovery and the challenge of clinical implementation.

Conventional antimicrobials are increasingly ineffective due to the emergence of multidrug-resistance among pathogenic microorganisms. The need to overcome these deficiencies has triggered exploration for novel and unconventional approaches to controlling microbial infections. Multidrug efflux systems (MES) have been a profound obstacle in the successful deployment of antimicrobials. The discovery of small molecule efflux system blockers has been an active and rapidly expanding research discipline. A major theme in this platform involves efflux pump inhibitors (EPIs) from natural sources. The discovery methodologies and the available number of natural EPI-chemotypes are increasing. Advances in our understanding of microbial physiology have shed light on a series of pathways and phenotypes where the role of efflux systems is pivotal. Complementing existing antimicrobial discovery platforms such as photodynamic therapy (PDT) with efflux inhibition is a subject under investigation. This core information is a stepping stone in the challenge of highlighting an effective drug development path for EPIs since the puzzle of clinical implementation remains unsolved. This review summarizes advances in the path of EPI discovery, discusses potential avenues of EPI implementation and development, and underlines the need for highly informative and comprehensive translational approaches.

Experimental and theoretical studies on the enantioselectivity of molecularly imprinted polymers prepared with a chiral functional monomer.

A comprehensive study on the enantioseparation of racemic bis[1-phenylethyl]amine (PEA) on a series of molecularly imprinted polymers (MIPs) prepared using the chiral functional monomer (S)-2-(2-methyl-acryloylamino)-3-phenyl propionic acid (MAPP) is reported. MIP-R, MIP-S and MIP-RS, were synthesized separately by imprinting the pure enantiomers (R-, S-PEA) and racemic PEA, respectively, MAPP, EDGMA as crosslinker and chloroform as the porogen. It was found that all MIPs prepared were able to resolve the PEA racemate. Residence times (t(r)) and enantioselectivity factors (α) were estimated from typical elution chromatography experiments. Frontal chromatography experiments were conducted to acquire the adsorption isotherms for both enantiomers on the different MIPs (and on the non-imprinted polymer, NIP). The adsorption isotherms were analyzed using the affinity spectrum (AS) and the expectation-maximization (EM) methods. The study also involved the theoretical evaluation of the MAPP/enantiomers interactions in the pre-polymer mixture. The EM method predicts mono- and bimodal distribution of affinity binding sites depending upon the polymer analyzed. Apparently, the enantioseparation process depends on relatively small differences in the stabilization of the diasteroisomeric ion-pairs PEA/MAPP complexes on the surface of the polymers.

Charge transfer properties of Tröger base derivatives.

Two triarylamine centers bridged through an aliphatic bridge feature unexpected charge transfer properties, bearing an important electronic coupling between them in the absence of a π linker; EPR, electrochemistry, electronic spectroscopy and first principles molecular calculations are combined to study the electronic structure of this compound.

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.

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.

Species with negative electron affinity and standard DFT methods. Finding the valence anions.

Recently, we have shown that traditional bound-electron DFT models are reliable enough to reproduce negative electron affinities (EA) within a few meV, as long as the valence anion state is found, but they seem to fail in predicting the lowest EA when the ground anion state obtained is non-valence, which holds the extra electron in a diffuse orbital around the molecule; here we propose an alternative approach for finding the valence anion state, based on the stabilization exerted by a polar solvent; the methodology yields correct EA values (i.e. beyond the Koopman's theorem approximation) by gradually decreasing the dielectric constant of the medium.

An experimental and theoretical study on the electrostatic effect of an appended cationic group on electronic properties of aromatic systems.

Tetraalkylammonium salts, characterized by an aromatic system pending from one of the alkyl chains, are taken as model systems to study the spectroscopic and redox properties of the aromatic centre under the field effects exerted by the charged group through alkyl bridges of varying length. The changes in the aromatic's redox properties, due to the net field effect and its different components, are interpreted on theoretical bases.

Inter- and intramolecular-bridge-mediated electron transfer in aliphatic halides.

The anionic surfaces of the 1-chloro- and 4-chlorobicyclo[2.2.1]heptan-2-one, 1-chloro- and 4-chlorobicyclo[2.2.2]octan-2-one, 1-chloro- and 5-chloroadamantan-2-one, and 2-chlorotricyclo[7.3.1.0(2,7)]tridecan-13-one were explored using DFT functionals with full geometry optimization in solution. The reductive cleavage of these compounds is controlled by the rigidity of the polycycle, its capability to form an unstrained radical, and by the relative carbonyl/C-Cl disposition on the bridge. Such control can be exerted by either a concerted-dissociative or a stepwise mechanism with radical anions as intermediates. 5-Chloroadamantan-2-one is the most suitable compound to follow the latter pathway.

Ab initio evaluation of intramolecular electron transfer reactions in halobenzenes and stabilized derivatives.

The potential energy surfaces for the fragmentation of the radical anions of p-nitrochlorobenzene and p- and m-chloroacetophenones were explored using first principle methods. The behavior of these compounds, stabilized by pi acceptors, is compared to that shown by the unsubstituted halobenzenes (PhX, X = F, Cl, Br, I). The presence of pi and sigma radical anions was inspected as well as the intramolecular electron transfer (intra-ET) from the pi to the sigma surface, responsible for the dissociation of these intermediates. The profiles obtained with the B3LYP functional in the gas phase and in the presence of a polar solvent are in agreement with the spectroscopic evidence and with the experimentally observed reactivity of the compounds under study. The stability of the radical anion of p-nitrochlorobenzene and the adiabatic and endothermic nature of its dissociation are explained. The order of the rate constants for dissociation m-chloroacetophenone < p-chloroacetophenone is interpreted on the basis of the differences in the adiabatic character of the intra-ET of both isomers which is ascribed to the nodal properties of their SOMOs. In the halobenzene family, the electronic factors responsible for the intra-ET are analyzed. The stabilization of the sigma surface exerted by the different halogens and its effect on the rate constants for dissociation are explained.