DFT studies of camptothecins cytotoxicity III: camptothecin, irinotecan and SN-38

Geometries of camptothecin, irinotecan, SN-38, and of their hypothetical Cu(II) complexes were optimized at the B3LYP/6-311G* level of theory. Their electron structure, evaluated in terms of Mulliken population analysis and Quantum Theory of Atoms-in-Molecule, was subsequently related to in vitro cytotoxicity. Electron density transfer from the relevant active sites to Cu decreases in the sequence irinotecan > SN-38 > camptothecin. The absolute values of their metal-ligand interaction energies exhibit the same trend. Discrepancy with the least relative in vitro cytotoxicity of irinotecan can be explained by differences in its pharmacokinetics.

Structural and photodynamic properties of the anti-cancer drug irinotecan in aqueous solutions of different pHs

This work reports on photophysical studies of the irinotecan (IRT) anti-cancer drug in water solutions of different acidities (pH = 1.11-9.46). We found that IRT co-exists as mono-cationic (C1), di-cationic (C2), or neutral (N) forms. The population of each prototropic species depends on the pH of the solution. At pH = 1.11-3.01, the C1 and C2 structures are stabilized. At pH = 7.00, the most populated species is C1, while at pH values larger than 9.46 the N form is the most stable species. In the 1.11-2.61 pH range, the C1* emission is efficiently quenched by protons to give rise to the emission from C2*. The dynamic quenching constant, KD, is ∼32 M-1. While the diffusion governs the rate of excited-state proton-transfer (ESPT) under these conditions, the reaction rate increases with the proton concentration. A two-step diffusive Debye-Smoluchowski model was applied at pH = 1.11-2.61 to describe the protonation of C1*. The ESPT time constants derived for C1* are 382 and 1720 ps at pH = 1.11 and 1.95, respectively. We found that one proton species is involved in the protonation of C1* to give C2*, in the analyzed acidic pH range. Under alkaline conditions (pH = 9.46), the N form is the most stable structure of IRT. These results indicate the influence of the pH of the medium on the structural and dynamical properties of IRT in water solution. They may help to provide a better understanding on the relationship between the structure and biological activity of IRT.

Probing the Characterization of the Interaction of Aflatoxins B1 and G1 with Calf Thymus DNA In Vitro

The binding characterization of aflatoxins with calf thymus DNA (ctDNA) under physiological conditions was investigated. Multispectroscopic techniques, ctDNA melting, viscosity measurements, and molecular docking techniques were employed to elucidate the binding mechanism of the aflatoxins with DNA. The fluorescence results indicated that both aflatoxin B1 (AFB1) and aflatoxin G1 (AFG1) bound to the ctDNA, forming complexes through hydrogen bonding. The binding constants of AFB1 and AFG1 with ctDNA reached up to 10³ L·mol-1 and 10⁴ L·mol-1, respectively, and AFG1 exhibited a higher binding propensity than that of AFB1. Furthermore, both AFB1 and AFG1 bound to the ctDNA through groove binding, as evidenced by the results of the spectroscopic, iodide quenching effect, viscosity, and ctDNA melting measurements. Changes in the circular dichroism signal manifested that both AFB1 and AFG1 induced an increase in the right-handed helicity, but only minimally influenced the base stacking of the DNA. A molecular docking study of the aflatoxin's binding with the DNA revealed a groove binding mode, which was driven mainly by hydrogen bonding. This study of aflatoxin-ctDNA interaction may provide novel insights into the toxicological effect of the mycotoxins.

Quinoxalines as potent selective CRFRs ligands for monitoring and brain diagnostic

The paper highlighted quinoxalines as potent ligands to corticotropin-releasing factor receptor types 1 and 2. The content includes design and structure-activity relationship of 50 model substances to CRFR1, CRFR2α and CRF2β, respectively. It is important to bear in mind, that our concept has based on challenging research task, designing for selective CRFRs ligands. Because,: (i) These macromolecules can bond more than one ligand, thus causing for a distinct physiological response; (ii) CRFRs also participate readily in protein-protein interactions; (iii) CRFRs have two step activation mechanism and; (iv) CRFR1 has low selectivity. In spite of, numerous research efforts, which have been devoted to the isolation of series peptidic and non-peptidic CRFRs agonists, the poor penetration across blood-brain barrier restricts, their wide application in the clinical practice. Furthermore, the biological role of CRFR2 is not yet fully understood. For that reason, the studies of the structure-activity relationship have significant impact in the field. The great advantages of quinoxalines as prospective ligands are based on their: (a) One-step synthetic road, using mild experimental conditions and, allowing to involve various functional groups in the molecular scaffold as well as good-to-excellent yields, employing Fischer and Hinsberg methods; (b) High selectivity to CRFRs sub-types and; (c) Tunable fluorescence emission within the frame of a large scale of the electromagnetic spectrum ∈ 500-700 nm.

Evodiamine and rutaecarpine alkaloids as highly selective transient receptor potential vanilloid 1 agonists

Despite that among non-camptothecin natural products promising anticancer therapeutics are evodiamine derivatives, involved into mechanism of physiological function of topoisomerase-I. But, more recent findings have been shown that substituted quinazole alkaloids act as transient receptor potential vanilloid 1 agonists. The TRP(V1) is a calcium ion channel, activated by pH, heat and inflammatory activators. I is implicated in pain sensing. TRPV1 agonist is capsaicine (1). Both 1 and evodiamine (2), therefore, produce same physiological response, but are structurally unrelated from chemical viewpoint. Furthermore precise mechanistic aspects of drugs receptor interactions are still not fully understood. This study is the first one, which provides assessment of molecular factors contributing significantly to selectivity of 2 and rutaecarpine (3) as well as their twenty-two new functionalized derivatives towards (TRP)V1. The suggested new functionalization type of molecular skeleton, which is completely different one in respect the known derivatives, which is implicated in treatment of variety of cancer cell lines interacting preferably with topoisomerase-I. It resulted to increasing of the binding affinity and selectivity of the functionalized derivatives specifically to (TRP)V1∈1.36-1.72 and ∈2.50-3.16 higher than 1-3.

Sequence selectivity of the cleavage sites induced by topoisomerase I inhibitors: a molecular dynamics study

Topoisomerase IB (Top1) inhibitors, such as camptothecin (CPT), stabilize the Top1-DNA cleavage complex in a DNA sequence-dependent manner. The sequence selectivity of Top1 inhibitors is important for targeting specific genomic sequences of therapeutic value. However, the molecular mechanisms underlying this selectivity remain largely unknown. We performed molecular dynamics simulations to delineate structural, dynamic and energetic features that contribute to the differential sequence selectivity of the Top1 inhibitors. We found the sequence selectivity of CPT to be highly correlated with the drug binding energies, dynamic and structural properties of the linker domain. Chemical insights, gained by per-residue binding energy analysis revealed that the non-polar interaction between CPT and nucleotide at the +1 position of the cleavage site was the major (favorable) contributor to the total binding energy. Mechanistic insights gained by a potential of mean force analysis implicated that the drug dissociation step was associated with the sequence selectivity. Pharmaceutical insights gained by our molecular dynamics analyses explained why LMP-776, an indenoisoquinoline derivative under clinical development at the National Institutes of Health, displays different sequence selectivity when compared with camptothecin and its clinical derivatives.

Hollow superparamagnetic iron oxide nanoshells as a hydrophobic anticancer drug carrier: intracelluar pH-dependent drug release and enhanced cytotoxicity

With curcumin and doxorubicin (DOX) base as model drugs, intracellular delivery of hydrophobic anticancer drugs by hollow structured superparamagnetic iron oxide (SPIO) nanoshells (hydrodynamic diameter: 191.9 ± 2.6 nm) was studied in glioblastoma U-87 MG cells. SPIO nanoshell-based encapsulation provided a stable aqueous dispersion of the curcumin. After the SPIO nanoshells were internalized by U-87 MG cells, they localized at the acidic compartments of endosomes and lysosomes. In endosome/lysosome-mimicking buffers with a pH of 4.5-5.5, pH-dependent drug release was observed from curcumin or DOX loaded SPIO nanoshells (curcumin/SPIO or DOX/SPIO). Compared with the free drug, the intracellular curcumin content delivered via curcumin/SPIO was 30 fold higher. Increased intracellular drug content for DOX base delivered via DOX/SPIO was also confirmed, along with a fast intracellular DOX release that was attributed to its protonation in the acidic environment. DOX/SPIO enhanced caspase-3 activity by twofold compared with free DOX base. The concentration that induced 50% cytotoxic effect (CC(50)) was 0.05 ± 0.03 μg ml(-1) for DOX/SPIO, while it was 0.13 ± 0.02 μg ml(-1) for free DOX base. These results suggested SPIO nanoshells might be a promising intracellular carrier for hydrophobic anticancer drugs.

On the Biosynthetic Pathway of Papaverine via (S)-Reticuline – Theoretical vs. Experimental Study

The electronic structures, optical properties and molecular structures of a series of isoquinoline alkaloids resulting in the formation of papaverine, through a proposed biosynthetic pathway via S(+)-reticuline were elucidated. The mechanism of papaverine synthesis was studied by electronic absorption, diffuse reflectance, fluorescence and CD spectroscopy, as well as ESI and MALDI Orbitrap imaging mass spectrometry. Quantum chemical DFT calculations in the gas phase and solution were performed with a view to study the electronic transitions of the interacting species, corresponding proposed intermediates, and the expected mass spectrometric fragments. The complete study and understanding of the mechanism of the biosynthetic pathway in the poppy plants appears important for the functional oriented drug-design and synthesis of corresponding structurally related alkaloids.

Physical Properties and Molecular Conformations of Indole Alkaloids and Model Protein Interactions – Theoretical vs. Experimental Study

The physical properties and molecular structure of five natural indole alkaloids (IAs) and their interaction with protein targets have been studied, experimentally and theoretically. Electronic absorption (EAs) and CD spectroscopy, electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS), as well as imaging mass spectrometric techniques (IMS) were used, analyzing the isolated alkaloids and corresponding IAs/protein molecular complexes. Theoretical quantum chemical DFT calculations were also applied. The mechanism of their biological activity and structure-activity relationship as potential neurologically active compounds were studied, using the model interactions with 5HT2A receptors. The gas-phase stable molecular fragments of the IAs are discussed comparing the experimental mass spectrometric data and theoretical quantum chemical DFT calculations of the different molecular fragments of the IAs.