Biophysical aspects and biological implications of the interaction of benzophenanthridine alkaloids with DNA

Small Molecule Targeting PPM1A Activates Autophagy for Mycobacterium tuberculosis Host-Directed Therapy

Mycobacterium tuberculosis (Mtb), the infectious agent of tuberculosis (TB), causes over 1.5 million deaths globally every year. Host-directed therapies (HDT) for TB are desirable for their potential to shorten treatment and reduce the development of antibiotic resistance. Previously, we described a modular biomimetic strategy to identify SMIP-30, targeting PPM1A (IC50 = 1.19 μM), a metal-dependent phosphatase exploited by Mtb to survive intracellularly. SMIP-30 restricted the survival of Mtb in macrophages and lungs of infected mice. Herein, we redesigned SMIP-30 to create SMIP-031, which is a more potent inhibitor for PPM1A (IC50 = 180 nM). SMIP-031 efficiently increased the level of phosphorylation of S403-p62 and the expression of LC3B-II to activate autophagy, resulting in the dose-dependent clearance of Mtb in infected macrophages. SMIP-031 possesses a good pharmacokinetic profile and oral bioavailability (F = 74%). In vivo, SMIP-031 is well tolerated up to 50 mg/kg and significantly reduces the bacteria burden in the spleens of infected mice.

Safety and efficacy of a feed additive consisting of Macleaya cordata (Willd.) R. Br. extract and leaves (Sangrovit® extra) for all poultry species (excluding laying and breeding birds) (Phytobiotics Futterzusatzstoffe GmbH)

Following a request from the European Commission, EFSA was asked to deliver a scientific opinion on the safety and efficacy of Macleaya cordata (Willd.) R. Br. extract and leaves (Sangrovit® Extra) when used as a zootechnical feed additive (functional group: other zootechnical additives) for all poultry species (excluding laying and breeding birds). The additive is standardised to contain a concentration of the sum of the four alkaloids sanguinarine, chelerythrine, protopine and allocryptopine of 1.25%, with 0.5% sanguinarine. Owing to the presence of the DNA intercalators sanguinarine and chelerythrine, a concern for genotoxicity was identified. The EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) had no safety concerns when the additive is used at the recommended level of 150 mg/kg complete feed (corresponding to 0.750 mg sanguinarine/kg complete feed) for chickens for fattening and other poultry species for fattening. No conclusion can be drawn for poultry reared for laying/breeding. The use of Sangrovit® Extra in poultry species for fattening at the maximum recommended level was considered of low concern for consumers. The additive was shown to be irritant to the eyes but not irritant to skin or a skin sensitiser. The FEEDAP Panel could not exclude the potential of the additive to be a respiratory sensitiser. When handling the additive, exposure of unprotected users to sanguinarine and chelerythrine may occur. Therefore, to reduce the risk, the exposure of users should be reduced. The use of Sangrovit® Extra as a feed additive under the proposed conditions of use was considered safe for the environment. The additive Sangrovit® Extra had the potential to be efficacious in improving performance of chickens for fattening at 45 mg/kg complete feed. This conclusion was extended to chickens reared for laying/breeding and extrapolated to all poultry species for fattening or reared for laying/breeding.

Computational Studies of the Photogeneration from Dihydrosanguinarine and the Probable Cytotoxicity Mechanism of Sanguinarine

A computational investigation of the mechanism of dihydrosanguinarine (DHSAN) photoactivation and its conversion into the active drug sanguinarine (SAN) is here reported. The reaction mechanism of DHSAN photoconversion was fully explored by considering its excitation first, essential for generating one of the reactants, the 1O2, and then locating all the minima and transition states involved in the formation of SAN. Both forms of the drug present at physiological pH, namely, iminium cation and alkanolamine, were considered as products of such reaction. The ability of the generated drug SAN to induce cell apoptosis was then explored, taking into consideration two anticancer activities: the induction of DNA conformational and functional changes by intercalation and the absorption of light with proper wavelength to trigger type II photochemical reactions leading to 1O2 sensitization for photodynamic therapy application. Concerning the ability to work as photosensitizers, the outcomes of our calculations prove that DHSAN can easily be converted into the active SAN under visible and NIR irradiation through the application of two-photon excitation, and that the maximum absorption of SAN, once intercalated into DNA, shifts to the near region of the therapeutic window.

Silver Catalyzed Decarbonylative [3 + 2] Cycloaddition of Cyclobutenediones and Formamides

As an important moiety in natural products, N,O-acetal has attracted wide attention in the past few years. An efficient method to construct N,O-acetal has been developed. Using silver catalyst, cyclobutenediones were smoothly converted to the corresponding γ-aminobutenolides in the presence of formamides, in which cyclobutenediones likely proceed with a key decarbonylative [3 + 2] cycloaddition process. In this way, a series of products with varied substituents were isolated in moderate yield and fully characterized.

Molecular insight into the binding aspects of benzo[c]phenanthridine alkaloid nitidine with bovine hemoglobin: A biophysical exploration

The association of a putative bioactive alkaloid nitidine (NIT) with blood protein bovine hemoglobin (BHb) was investigated by employing various biophysical and molecular docking techniques. NIT binding to BHb was first characterized by hypochromic effect on the Soret band absorption of BHb from spectrophotometric studies. Spectrofluorimetric titration and unchanged fluorescence lifetime of BHb confirmed ground state complexation followed by the static nature of the emission quenching mechanism of the protein induced by NIT. Substantial conformational changes in the protein structure were established from circular dichroism study. Conformational perturbation results a lowering in the α-helical organization of the tetrameric protein structure. Thermodynamics of the binding suggest that the binding is exothermic with a favourable small positive entropy change and negative enthalpy change making a sense of electrostatic interaction as the major acting force. Experimentally calculated free energy change for the NIT-BHb interaction was found to be -7.50 kcal mol^-1 which is in well agreement to the theoretical docking energy value of -6.36 kcal mol^-1. AutoDock based molecular docking suggests the internal cavity of BHb as the preferred binding position of NIT. Overall this manuscript depicts consequences on the molecular interaction of NIT with BHb from structural and energetic standpoints providing a profound insight into protein-ligand association.

Modulation of DNA structure formation using small molecules

Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.

Investigation of hairpin DNA and chelerythrine interaction by a single bio-nanopore sensing interface

Chelerythrine (CHE) is one of the potential drugs for cancer treatments. The interaction between hairpin DNA and CHE has been investigated by spectral and mass spectrometry methods. In this paper, the stability of hairpin DNA with different loop bases and its interaction with CHE were explored with a single α-hemolysin (α-HL) nanopore sensing interface. The results showed that the characteristic current pulses not only relate to the loop composition changes of the hairpin DNA, but also provide interaction information between CHE and the hairpin DNA molecules. The dwell time of current pulses for hairpin DNA was significantly increased (hundreds of ms) due to the addition of CHE, and two characteristic current distributions were recognized for the hairpin with T₃ and C₃ loops. The two characteristic current groups could be ascribed to the hairpin DNA and the ones with CHE. This study indicates that it is possible to study the interaction between single CHE and single hairpin DNA molecules by the single-nanopore sensing interface as an alternative method to conventional spectrometric methods for therapeutic mechanism and drug screening purposes.

Palladium-catalyzed enantioselective C(sp2)–H arylation of ferrocenyl ketones enabled by a chiral transient directing group

A carboxylate-assisted palladium-catalyzed enantioselective C(sp²)–H arylation of ferrocenyl ketones is achieved through utilizing catalyticl-tert-leucine as a chiral transient directing group.

Natural isoquinoline alkaloids: binding aspects to functional proteins, serum albumins, hemoglobin, and lysozyme

The putative anticancer alkaloids berberine, palmatine, jatrorrhizine, and sanguinarine are known to bind to nucleic acids. To develop them as potential drugs for therapeutic use, their binding affinity to functional proteins and mode of transport in the circulatory system need to be clearly understood. Towards this, many studies on their binding aspects to proteins have been reported and a considerable amount of data, mostly of biophysical nature, exists in the literature. The importance of these natural isoquinoline alkaloids and the recent literature on their interaction phenomena with functional proteins, serum albumins, hemoglobin, and lysozyme are presented in this review.

6-Acetonyldihydrochelerythrine Is a Potent Inducer of Apoptosis in HCT116 and SW620 Colon Cancer Cells

6-Acetonyldihydrochelerythrine (1), a benzophenanthridine alkaloid, isolated from the methanol extract of Zanthoxylum capense, displayed potent cytotoxic activity in human HCT116 and SW620 colon carcinoma cells, to a higher extent than 5-fluorouracil (5-FU), the cornerstone chemotherapeutic agent in colon cancer. Cytotoxicity of 1 was evaluated by MTS, lactate dehydrogenase (LDH), and Guava ViaCount assays. Interestingly, 1 significantly induced cytotoxicity in both cell lines, leading to a significant increase in LDH release, as compared to 5-FU. Further, Guava ViaCount flow cytometry assays demonstrated that 1 significantly increased cell death, as shown by the presence of a significantly higher population of apoptotic cells in both cell lines, as compared to cells exposed to 5-FU. Furthermore, evaluation of nuclear morphology by Hoechst staining of 1-treated HCT116 and SW620 cells confirmed flow cytometry results, demonstrating a marked induction of apoptotic cell death by 1, again to a further extent than that elicited by 5-FU. In addition, immunoblot analysis to ascertain the molecular events triggered by 1 exposure was performed. The results show that 1 exposure reduced the steady-state expression and activation of the pro-survival proteins ERK5 and Akt and increased the steady-state expression of p53 in both HCT116 and SW620 cells. Changes in ERK5 or Akt activation can be ascertained by evaluating the ratio of p-ERK5/ERK5 or p-Akt/Akt. In addition, exposure to 1 reduced expression of XIAP, Bcl-XL, and Bcl-2, while increasing the cleavage of poly(ADP-ribose) polymerase in both cell lines. Collectively, the data indicate that 6-acetonyldihydrochelerythrine (1) is a potent inducer of apoptosis in HCT116 and SW620 cell lines, highlighting its potential relevance in colon cancer.

Fluorescence quenching investigation on the interaction of glutathione-CdTe/CdS quantum dots with sanguinarine and its analytical application

Water-soluble glutathione (GSH)-capped core/shell CdTe/CdS quantum dots (QDs) were synthesized. In pH5.4 sodium phosphate buffer medium, the interaction between GSH-CdTe/CdS QDs and sanguinarine (SA) was investigated by spectroscopic methods, including fluorescence spectroscopy and ultraviolet-visible absorption spectroscopy. Addition of SA to GSH-CdTe/CdS QDs results in fluorescence quenching of GSH-CdTe/CdS QDs. Quenching intensity was in proportion to the concentration of SA in a certain range. Investigation of the quenching mechanism, proved that the fluorescence quenching of GSH-CdTe/CdS QDs by SA is a result of electron transfer. Based on the quenching of the fluorescence of GSH-CdTe/CdS QDs by SA, a novel, simple, rapid and specific method for SA determination was proposed. The detection limit for SA was 3.4 ng/mL and the quantitative determination range was 0.2-40.0 µg/mL with a correlation coefficient of 0.9988. The method has been applied to the determination of SA in synthetic samples and fresh urine samples of healthy human with satisfactory results.

DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift

Small molecules that can specifically bind to a DNA abasic site (AP site) have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG), a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.

Binding of the anticancer alkaloid sanguinarine with tRNA(phe): spectroscopic and calorimetric studies

The interaction of the natural plant alkaloid and anticancer agent sanguinarine with tRNA(phe) has been investigated by spectroscopic and calorimetric techniques. Sanguinarine iminium binds to tRNA(phe) cooperatively; alkanolamine does not bind but in presence of large tRNA(phe) concentration, a conversion from alkanolamine to iminium occurs resulting in concomitant binding of the latter. The binding affinity of the iminium to tRNA(phe) obtained from isothermal titration calorimetry was of the order of 10(5) M(-1), which is close to that evaluated from spectroscopy. The binding was driven largely by negative enthalpy and a smaller but favourable positive entropy change. The binding was dependent on the [Na(+)] concentration, but had a larger non-electrostatic contribution to the Gibbs energy. A small heat capacity value and the enthalpy-entropy compensation in the energetics of the interaction characterized the binding of the iminium form to tRNA(phe). This study confirms that the tRNA(phe) binding moiety is the iminium form of sanguinarine.

Interaction of the anticancer plant alkaloid sanguinarine with bovine serum albumin

Background

Interaction of the iminium and alkanolamine forms of sanguinarine with bovine serum albumin (BSA) was characterized by spectroscopic and calorimetric techniques.

Methodology/Principal Findings

Formation of strong complexes of BSA with both iminium and alkanolamine forms was revealed from fluorescence quenching of sanguinarine. Binding parameters calculated from Stern-Volmer quenching method revealed that the neutral alkanolamine had higher affinity to BSA compared to the charged iminium form. Specific binding distances of 3.37 and 2.38 nm between Trp 212 (donor) and iminium and alkanolamine forms (acceptor), respectively, were obtained from Forster resonance energy transfer studies. Competitive binding using the site markers warfarin and ibuprofen, having definite binding sites, demonstrated that both forms of sanguinarine bind to site I (subdomain IIA) on BSA. Sanguinarine binding alters protein conformation by reducing the α-helical organization and increasing the coiled structure, indicating a small but definitive partial unfolding of the protein. Thermodynamic parameters evaluated from isothermal titration calorimetry suggested that the binding was enthalpy driven for the iminium form but favoured by negative enthalpy and strong favourable entropy contributions for the alkanolamine form, revealing the involvement of different molecular forces in the complexation.

Conclusions/Significance

The results suggest that the neutral alkanolamine form binds to the protein more favourably compared to the charged iminium, in stark contrast to the reported DNA binding preference of sanguinarine.

Binding of the anticancer alkaloid sanguinarine to double stranded RNAs: insights into the structural and energetics aspects

Elucidation of the molecular aspects of small molecule-RNA complexation is of prime importance for rational RNA targeted drug design strategies. Towards this, the interaction of the cytotoxic plant alkaloid sanguinarine to three double stranded ribonucleic acids, poly (A).poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical and thermodynamic techniques. Absorbance and fluorescence studies showed that the alkaloid bound cooperatively to these RNAs with binding affinities of the order 10(4) M(-1). Fluorescence quenching and hydrodynamic studies gave evidence for intercalation of sanguinarine to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity values obtained from spectroscopic data. The binding of sanguinarine stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of sanguinarine to these double stranded RNAs varied in the order, poly(A).poly(U) > poly(I).poly(C) >> poly(C).poly(G). The temperature dependence of the enthalpy changes afforded negative values of heat capacity changes for the binding of sanguinarine to poly(A).poly(U) and poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation phenomena was also seen in poly(A).poly(U) and poly(I).poly(C) systems that correlated to the strong binding involving a multiplicity of weak noncovalent interactions compared to the weak binding with poly(C).poly(G). These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.