Interaction of isoquinoline alkaloids with polymorphic DNA structures

Interaction of isoquinoline alkaloids with pyrimidine motif triplex DNA by mass spectrometry and spectroscopies reveals diverse mechanisms

Isoquinoline alkaloids represent an important class of molecules due to their broad range of pharmacology and clinical utility. Prospective development and use of these alkaloids as effective anticancer agents have elicited great interest. In this study, in order to reveal structure-activity relationship, we present the characterization of bioactive isoquinoline alkaloid-DNA triplex interactions, with particular emphasis on the sequence selectivity and preference of binding to the two types of DNA triplexes, by electrospray ionization mass spectrometry (ESI-MS) and various spectroscopic techniques. The six alkaloids, including coptisine, columbamine, epiberberine, berberrubine, jateorhizine, and fangchinoline, were selected to explore their interactions with the TC and TTT triplex DNA structures. Berberrubine, fangchinoline, coptisine, columbamine, and epiberberine have preference for TC rich DNA sequences compared to TTT rich DNA triplex based on affinity values in MS. The experimental results from different fragmentation modes in tandem MS, subtractive and hyperchromic effects in UV absorption spectra, fluorescence quenching and enhancement in fluorescence spectra, and strong conformational changes in circular dichroism (CD) hinted that the interaction between isoquinoline alkaloid-TC/TTT DNA had diverse mechanisms including at least two different binding modes: the electrostatic binding and the intercalation binding. Interestingly, columbamine, berberrubine, and fangchinoline can stabilize TTT triplex as inferred from optical thermal melting profiles, while it was not the case in TC triplex. These results provide new insights into binding of isoquinoline alkaloids to pyrimidine motif triplex DNA.

Interaction of the tetracyclines with double-stranded RNAs of random base sequence: new perspectives on the target and mechanism of action

The 16S rRNA binding mechanism proposed for the antibacterial action of the tetracyclines does not explain their mechanism of action against non-bacterial pathogens. In addition, several contradictory base pairs have been proposed as their binding sites on the 16S rRNA. This study investigated the binding of minocycline and doxycycline to short double-stranded RNAs (dsRNAs) of random base sequences. These tetracyclines caused a dose-dependent decrease in the fluorescence intensities of 6-carboxyfluorescein (FAM)-labelled dsRNA and ethidium bromide (EtBr)-stained dsRNA, indicating that both drugs bind to dsRNA of random base sequence in a manner that is competitive with the binding of EtBr and other nucleic acid ligands often used as stains. This effect was observable in the presence of Mg(2+). The binding of the tetracyclines to dsRNA changed features of the fluorescence emission spectra of the drugs and the CD spectra of the RNA, and inhibited RNase III cleavage of the dsRNA. These results indicate that the double-stranded structures of RNAs may have a more important role in their interaction with the tetracyclines than the specific base pairs, which had hitherto been the subject of much investigation. Given the diverse functions of cellular RNAs, the binding of the tetracyclines to their double-stranded helixes may alter the normal processing and functioning of the various biological processes they regulate. This could help to explain the wide range of action of the tetracyclines against various pathogens and disease conditions.

New 13-pyridinealkyl berberine analogues intercalate to DNA and induce apoptosis in HepG2 and MCF-7 cells through ROS mediated p53 dependent pathway: biophysical, biochemical and molecular modeling studies

A new series of 13-pyridinealkyl berberine analogues was synthesized and their DNA binding efficacy studied by employing spectroscopic, calorimetric and molecular modeling techniques.

Ethnobotany, phytochemistry and pharmacology of Stephania rotunda Lour

ETHNOPHARMACOLOGICAL RELEVANCE

Stephania rotunda Lour. (Menispermaceae) is an important traditional medicinal plant that is grown in Southeast Asia. The stems, leaves, and tubers have been used in the Cambodian, Lao, Indian and Vietnamese folk medicine systems for years to treat a wide range of ailments, including asthma, headache, fever, and diarrhoea.

AIM OF THE REVIEW

To provide an up-to-date, comprehensive overview and analysis of the ethnobotany, phytochemistry, and pharmacology of Stephania rotunda for its potential benefits in human health, as well as to assess the scientific evidence of traditional use and provide a basis for future research directions.

MATERIAL AND METHODS

Peer-reviewed articles on Stephania rotunda were acquired via an electronic search of the major scientific databases (Pubmed, Google Scholar, and ScienceDirect). Data were collected from scientific journals, theses, and books.

RESULTS

The traditional uses of Stephania rotunda were recorded in countries throughout Southeast Asia (Cambodia, Vietnam, Laos, and India). Different parts of Stephania rotunda were used in traditional medicine to treat about twenty health disorders. Phytochemical analyses identified forty alkaloids. The roots primarily contain l-tetrahydropalmatine (l-THP), whereas the tubers contain cepharanthine and xylopinine. Furthermore, the chemical composition differs from one region to another and according to the harvest period. The alkaloids exhibited approximately ten different pharmacological activities. The main pharmacological activities of Stephania rotunda alkaloids are antiplasmodial, anticancer, and immunomodulatory effects. Sinomenine, cepharanthine, and l-stepholidine are the most promising components and have been tested in humans. The pharmacokinetic parameters have been studied for seven compounds, including the three most promising compounds. The toxicity has been evaluated for liriodenine, roemerine, cycleanine, l-tetrahydropalmatine, and oxostephanine.

CONCLUSION

Stephania rotunda is traditionally used for the treatment of a wide range of ailments. Pharmacological investigations have validated different uses of Stephania rotunda in folk medicine. The present review highlights the three most promising compounds of Stephania rotunda, which could constitute potential leads in various medicinal fields, including malaria and cancer.

Photophysical and calorimetric studies on the binding of 9-O-substituted analogs of the plant alkaloid berberine to double stranded poly(A)

This interaction of four novel 9-O-substituted analogs of the plant alkaloid berberine with double stranded poly(A) was studied using a variety of biophysical techniques. Remarkably higher binding of two 9-O-ω-amino alkyl ether analogs compared to the two 9-O-N-aryl/arylalkyl amino carbonyl methyl berberine analogs was observed. Quantum efficiency values suggested that energy was transferred from the adenine base pairs to the analogs on binding. Ferrocyanide quenching and viscosity studies revealed the binding mode to be intercalative for these analogs. Circular dichroism studies showed that these analogs induced significant conformational changes in the secondary structure of ds poly(A). Energetics of the binding suggested that 9-O-N-aryl/arylalkyl amino carbonyl methyl berberines bound very weakly to ds poly(A). The binding of 9-O-ω-amino alkyl ether analogs was entropy dominated with a smaller but favorable enthalpic contribution to the Gibbs energy. Increasing the temperature resulted in weaker binding; the enthalpic contribution increased and the entropic contribution decreased. A small negative heat capacity change with significant enthalpy-entropy compensation established the involvement of multiple weak noncovalent interactions in the binding process.

Study on noncovalent complexes of alkaloids with DNA duplex using electrospray ionization mass spectrometry

RATIONALE

DNA is an important molecular target in modern medicine research. Some DNA-binding ligands have been used to treat numerous diseases. Therefore, understanding the interactions of different ligands with DNA and looking for new DNA agents are necessary to develop new drugs.

METHODS

Electrospray ionization mass spectrometry (ESI-MS) in the negative ion mode was used to screen the noncovalent complexes between 11 alkaloids with double helix oligonucleotides at molar ratios 1:1 to 1:4. The relative binding affinities based on the fraction of bound DNA and sequence selectivities of alkaloids towards the duplex were also investigated by ESI-MS. Moreover, tandem mass spectrometry of 5-charged complex ions was used to try to determine DNA-binding modes.

RESULTS

Six alkaloids showed complexation with the selected DNA duplex, i.e., berberine, coptisine, peimine, aconitine, oxysophoridine and cytisine. They showed their binding affinities with d(AACTCCCGGCACAC/GTGTGCCGGGAGTT) in the order of berberine > coptisine > peimine > aconitine, oxysophoridine > cytosine; additional experiments involving collision energy proved this result. Sequence selectivities were not apparent for coptisine, peimine, aconitine and oxysophoridine with four DNA duplexes. The complexes containing berberine and coptisine underwent the predominant loss of the G base. However, for complexes containing the other four alkaloids, they dissociated via the loss of neutral drug. The results confirmed that they may have different binding modes.

CONCLUSIONS

According to experiment data and structural information, the binding mode of individual drugs with DNA was speculated. It was noted that the bindings of alkaloids peimine, aconitine and oxysophoridine with DNA are discovered firstly. This may give a clue to design duplex-binding ligands and be helpful for understanding biological activities of these alkaloids.

Polymorphic nucleic Acid binding of bioactive isoquinoline alkaloids and their role in cancer

Bioactive alkaloids occupy an important position in applied chemistry and play an indispensable role in medicinal chemistry. Amongst them, isoquinoline alkaloids like berberine, palmatine and coralyne of protoberberine group, sanguinarine of the benzophenanthridine group, and their derivatives represent an important class of molecules for their broad range of clinical and pharmacological utility. In view of their extensive occurrence in various plant species and significantly low toxicities, prospective development and use of these alkaloids as effective anticancer agents are matters of great current interest. This review has focused on the interaction of these alkaloids with polymorphic nucleic acid structures (B-form, A-form, Z-form, H^L-form, triple helical form, quadruplex form) and their topoisomerase inhibitory activity reported by several research groups using various biophysical techniques like spectrophotometry, spectrofluorimetry, thermal melting, circular dichroism, NMR spectroscopy, electrospray ionization mass spectroscopy, viscosity, isothermal titration calorimetry, differential scanning calorimetry, molecular modeling studies, and so forth, to elucidate their mode and mechanism of action for structure-activity relationships. The DNA binding of the planar sanguinarine and coralyne are found to be stronger and thermodynamically more favoured compared to the buckled structure of berberine and palmatine and correlate well with the intercalative mechanism of sanguinarine and coralyne and the partial intercalation by berberine and palmatine. Nucleic acid binding properties are also interpreted in relation to their anticancer activity.