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 β2

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 β2 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 β2 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.

Impact of benzannulation on ESIPT in 2-(2'-hydroxyphenyl)-oxazoles: a unified perspective in terms of excited-state aromaticity and intramolecular charge transfer

Hydroxyphenyl-azoles are among the most popular ESIPT (Excited State Intramolecular Proton Transfer) scaffolds and as such, they have been thoroughly studied. Nevertheless, some aspects regarding the interplay between the emissive properties of these fluorophores and the size of their π-conjugated framework remain controversial. Previous studies have demonstrated that benzannulation of 2′-hydroxyphenyl-oxazole at the phenol group of the molecule can lead to either red- or blue-shifted fluorescence emission, depending on the site where it occurs. In this report, benzannulation at the heterocyclic unit (the oxazole site) is analysed in order to get the whole picture. The extension of π-conjugation does not significantly affect the ESIPT emission wavelength, but it leads instead to higher energy barriers for proton transfer in the first excited singlet state, as a consequence of dramatic changes in the charge transfer character of excitation caused by successive benzannulation. Theoretical calculations revealed an interesting connection between intramolecular charge transfer and excited-state aromaticity in the S₁ state. The theoretical approach presented herein allows the behaviour of hydroxyphenyl-oxazoles in the excited state to be rationalized and, more generally, a deeper understanding of the factors governing the ESIPT process to be obtained, a crucial point in the design of new and efficient fluorophores.

Benzannulation of a typical fluorophore reveals the interplay between ESIPT, excited-state aromaticity and intramolecular charge transfer.

Adiabatic deprotonation as an important competing pathway to ESIPT in photoacidic 2-phenylphenols

ESIPT (Excited State Intramolecular Proton Transfer) to C atom in 2-phenylphenol is known to be an intrinsically inefficient process. However, to the best of our knowledge, a structure-ESIPT efficiency relationship has not been elucidated yet. Here, we show that there exists a competitive interplay between photoacidity and ESIPT efficiency for the 2-phenylphenol system. The attachment of electron withdrawing groups to the phenol moiety promotes adiabatic deprotonation in the excited state and diminishes the charge transfer character of the excitations, and both these factors contribute in decreasing the ESIPT reaction yield. On the other hand, unfavorable conformational distribution in the ground state also appears as another important aspect responsible for the low ESIPT extent of 2-phenylphenol. A new derivative bearing electron donating, bulky substituents at ortho and para positions of the phenol ring shows an outstanding ESIPT performance, which demonstrates that the efficiency of the process can be significantly enhanced by modifying the substitution pattern. We anticipate that our results will help to guide the molecular designing of new compounds with high ESIPT efficiency.

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.

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.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2348-2) contains supplementary material, which is available to authorized users.

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

“And the winner is…” This work assesses the ability of different Density Functional Theory (DFT) functionals for a proper treatment of organic anionic species.

Gas-phase synthesis of 3-carboethoxy-quinolin-4-ones. A comprehensive computational mechanistic study to uncover the dark side of the Gould–Jacobs reaction

A set of 3-carboethoxy-quinolin-4-ones were synthesized from diethyl 2-((arylamino)methylene) malonates through a Gould–Jacobs cyclization using flash vacuum pyrolysis (FVP). A detailed mechanistic study was done using DFT and Coupled Clusters models.

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.

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.

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.

Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila

The zinc enzymes metallo beta-lactamases counteract the beneficial action of beta-lactam antibiotics against bacterial infections, by hydrolyzing their beta-lactam rings. To understand structure/function relationships on a representative member of this class, the B2 M beta L CphA, we have investigated the H-bond pattern at the Zn enzymatic active site and substrate binding mode by molecular simulation methods. Extensive QM calculations at the DFT-BLYP level on eleven models of the protein active site, along with MD simulations of the protein in aqueous solution, allow us to propose two plausible protonation states for the unbound enzyme, which are probably in equilibrium. Docking procedures along with MD simulations and QM calculations suggest that in the complex between the enzyme and its substrate (biapenem), the latter is stable in only one of the two protonation states, in addition it exhibits two different binding modes, of which only one agrees with previous proposals. In both cases, the substrate is polarized as in aqueous solution. We conclude that addressing mechanistic issues on this class of enzymes requires a careful procedure to assign protonation states and substrate docking modes.

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.