A theoretical and experimental study on the molecular and electronic structures of artemisinin and related drug molecules

DELTA50: A Highly Accurate Database of Experimental 1H and 13C NMR Chemical Shifts Applied to DFT Benchmarking

Density functional theory (DFT) benchmark studies of ¹H and ¹³C NMR chemical shifts often yield differing conclusions, likely due to non-optimal test molecules and non-standardized data acquisition. To address this issue, we carefully selected and measured ¹H and ¹³C NMR chemical shifts for 50 structurally diverse small organic molecules containing atoms from only the first two rows of the periodic table. Our NMR dataset, DELTA50, was used to calculate linear scaling factors and to evaluate the accuracy of 73 density functionals, 40 basis sets, 3 solvent models, and 3 gauge-referencing schemes. The best performing DFT methodologies for ¹H and ¹³C NMR chemical shift predictions were WP04/6-311++G(2d,p) and ωB97X-D/def2-SVP, respectively, when combined with the polarizable continuum solvent model (PCM) and gauge-independent atomic orbital (GIAO) method. Geometries should be optimized at the B3LYP-D3/6-311G(d,p) level including the PCM solvent model for the best accuracy. Predictions of 20 organic compounds and natural products from a separate probe set had root-mean-square deviations (RMSD) of 0.07 to 0.19 for ¹H and 0.5 to 2.9 for ¹³C. Maximum deviations were less than 0.5 and 6.5 ppm for ¹H and ¹³C, respectively.

Scalable and Predictive Spectra of Correlated Molecules with Moment Truncated Iterated Perturbation Theory

A reliable and efficient computation of the entire single-particle spectrum of correlated molecules is an outstanding challenge in the field of quantum chemistry, with standard density functional theory approaches often giving an inadequate description of excitation energies and gaps. In this work, we expand upon a recently introduced approach that relies on a fully self-consistent many-body perturbation theory coupled to a nonperturbative truncation of the effective dynamics at each step. We show that this yields a low-scaling and accurate method across a diverse benchmark test set that is capable of treating moderate levels of strong correlation effects, and we detail an efficient implementation for applications involving up to ∼1000 orbitals on parallel resources. We then use this method to characterize the spectral properties of the antimalarial drug molecule artemisinin, resolving discrepancies in previous works concerning the active sites of the lowest-energy fundamental excitations of the system.

Bioinspired Microenvironment Responsive Nanoprodrug as an Efficient Hydrophobic Drug Self-Delivery System for Cancer Therapy

Artemisinin compounds have shown satisfactory safety records in anti-malarial clinical practice over decades and have revealed value as inexpensive anti-tumor adjuvant chemotherapeutic drugs. However, the rational design and precise preparation of nanomedicines based on the artemisinin drugs are still limited due to their non-aromatic and fragile chemical structure. Herein, a bioinspired coordination-driven self-assembly strategy was developed to manufacture the artemisinin-based nanoprodrug with a significantly increased drug loading efficacy (∼70 wt %) and decreased preparation complexity compared to conventional nanodrugs. The nanoprodrug has suitable size distribution and robust colloidal stability for cancer targeting in vivo. The nanoprodrug was able to quickly disassemble in the tumor microenvironment with weak acidity and a high glutathione concentration, which guarantees a better tumor inhibitory effect than direct administration and fewer side effects on normal tissues in vivo. This work highlights a new strategy to harness a robust, simplified, organic solvent-free, and highly repeatable route for nanoprodrug manufacturing, which may offer opportunities to develop cost-effective, safe, and clinically available nanomedicines.

New Techniques of Structure Elucidation for Sesquiterpenes

The most significant new techniques that have been used in the twenty-first century for the structure elucidation of sesquiterpenes and some derivatives are reviewed in this chapter. A distinctive feature of these methodologies is the combination of accurate experimental measurements with theoretical data obtained by molecular modeling calculations that allow to visualize, understand, and quantify many structural characteristics. This has been the case for NMR spectroscopy, which has expanded its potential for solving complex structural problems by means of comparison with quantum mechanical molecular models. Ab initio and density functional theory calculations of chemical shifts, coupling constants, and residual chemical shift anisotropies have played important roles in the solution of many structures of sesquiterpenes. The assignments of their absolute configurations by evaluation of calculated and experimental chiroptical properties as electronic and vibrational circular dichroism are also reviewed. This chapter also includes the use of X-ray diffraction analysis with emphasis on calculations of the Flack and Hooft parameters, which are applicable to all molecules that crystallize in non-centrosymmetric space groups. The accurate molecular models of sesquiterpenes, validated by concordance with their experimental properties, are nowadays essential for the interpretation of the effects of these natural products on biological systems.

Can the Electron-Accepting Properties of Odorants Be Involved in Their Recognition by the Olfactory System?

The present study examines the possible importance of the electron-accepting properties of odorant molecules and, in particular, the formation and decay of temporary negative ions via low-energy electron attachment as a possible contribution toward understanding odorant recognition by olfactory receptors (ORs). Fragments formed by dissociative electron attachment (DEA) of mustard oil odorants represented by a series of isothiocyanates are studied experimentally using DEA spectroscopy and DFT calculations. Relative intensities for the most abundant fragment species, S^- and SCN^-, are found to be characteristic of structurally similar odorants under investigation. This novel approach for the investigation of odorants may contribute to understanding the initial stages of the olfactory process and may provide a means to distinguish between odorants and their interactions with the olfactory receptor system.

Low-Energy Electron Interaction with Melatonin and Related Compounds

The electron attaching properties and fragmentation of temporary negative ions of melatonin and its biosynthetic precursor tryptophan are studied in vacuo using dissociative electron attachment (DEA) spectroscopy. The experimental findings are interpreted in silico with the support of Hartree-Fock and density functional theory calculations of empty orbital energies and symmetries, and evaluation of the electron affinities of the indolic molecules under investigation. The only fragment anions formed by DEA to melatonin at incident electron energies below 2 eV are associated with the elimination of a hydrogen atom (energetically favored from the NH site of the pyrrole ring, leaving the ring intact) or a CH₃^· radical from the temporary molecular negative ion. Opening of the pyrrole ring of melatonin is not detected over the whole electron energy range of 0-14 eV. The DEA spectra of l- and d-tryptophan are almost identical under the present experimental conditions. The adiabatic electron affinity of melatonin is predicted to be -0.49 eV at the B3LYP/6-31+G(d) level, indicating that the DEA mechanism in melatonin is likely to be present in most life forms given the availability of low energy electrons in living systems in both plant and animal kingdoms. In particular, H atom donation usually associated with free-radical scavenging activity can be stimulated by electron attachment and N-H bond cleavage at electron energies around 1 eV.

Effects of different concentrations of artemisinin and artemisinin-iron combination treatment on Madin Darby Canine Kidney (MDCK) cells

Artemisinin is a sesquitrepenelactone with an endoperoxide bridge. It is a naturally occurring substance from Artemisia species plants. Artemisia species have been used in oriental medicine for centuries to treat malaria, gastrointestinal helminthosia, diarrhea, and as an antipyretic and sedative agent. Antileishmanial activity of the plants has been announced a few years ago. Dogs are the most important reservoir of leishmaniasis in some parts of the world. To use it as an antileishmanial drug in dogs, its side effects on different organs, among them the kidney as the organ of elimination have to be elucidated. Artemisinin with different concentrations (0.15, 0.3, 0.6 and 1.2 μg/ml) was added to the culture of MDCK (Madin darby canine kidney) cells with and without iron (86 μg/dl). All the changes were controlled and photographed every 12 hours using an invert microscope. After 60 hours, supernatants and cell extracts were examined for LDH (lactate dehydrogenase) concentration and total protein. Also TBARS (thiobarbituric acid reactive substances) test was performed on cell extracts. Some microscopic slides were prepared from the cells and stained with hematoxylin-eosin for microscopic exams. Biochemical parameters showed cellular reaction and injury in a concentration dependent manner. Cell injury was more severe in the iron-added groups. Microscopic exams showed cell and nuclear swelling, granular degeneration, vacuole and vesicle formation, cellular detachment, piknosis, karyorrhexis, cellular necrosis and inhibition of new mitosis. On using the drug for leishmaniasis treatment in the dog, it should be done with caution and supervision.

A new class of antimalarial dioxanes obtained through a simple two-step synthetic approach: rational design and structure-activity relationship studies

A new series of simple endoperoxides, characterized by a 3-methoxy-1,2-dioxane scaffold, was designed on the basis of a previously developed pharmacophore. Through a simplified and versatile scheme of synthesis, which utilizes cheap and commercially available starting materials, it was possible to obtain several structurally and stereochemically different compounds that were tested against P. falciparum. Most of compounds showed antimalarial activity in the low micromolar range and no cellular toxicity, all being significantly more active on chloroquine resistant (CQ-R) than on chloroquine sensitive (CQ-S) strains. Resulting structure-activity relationships were analyzed by means of experimental and computational techniques, validating our design rationale and tailoring it for the new scaffold. Our study demonstrated that according to the hypothesized mechanism of action, the antimalarial activity can be improved through rational structural modifications, paving the way for the development of new simplified antimalarial endoperoxides.

Effects of artemisinin in broiler chickens following chronic oral intake

Artemisinin has been used for centuries to treat malaria, intestinal tract helminthosis, diarrhea, and used as an antipyretic and sedative agent, but the usage in veterinary medicine is a new field. Recently, it has been used successfully to control experimental poultry coccidiosis. The present study aimed to determine the effects of different doses of artemisinin in broiler chickens with chronic usage. Sixty birds divided into one control and four treatment groups that fed rations mixed with artemisinin at doses of 17, 34, 68, and 136 ppm for 36 days. During the experiment, birds showed no clinical signs except anemia. In microscopic examinations, heart, lung, and spleen had no lesion, but liver, kidney, and brain showed various lesions. Degenerative lesions like intracytoplasmic eosinophilic inclusions were seen in both kidney and liver but fatty change was seen only in liver. There was no relationship between severity of the liver lesions and drug dosage. Central chromatolysis, scattered neuronal necrosis, and mild spongy changes were observed in five regions of the brain that were chosen for sectioning (motor cortex, cerebellar nuclei, midbrain nuclei, and hindbrain nuclei at two separate levels). Severity of lesions in brain was dose-dependent, and cerebral cortex was the most vulnerable area. Haematologic tests showed lower values for hematocrit and red blood cell count dose-dependently. In conclusion, artemisinin is a promising drug for prevention and control of coccidiosis in broiler chickens and its side effects are not too much serious especially at therapeutic doses.

A topological study of the decomposition of 6,7,8-trioxabicyclo[3.2.2]nonane induced by Fe(II): modeling the artemisinin reaction with heme

We report a theoretical study on the electronic and topological aspects of the reaction of dihydrated Fe(OH)(2) with 6,7,8-trioxabicyclo[3.2.2]nonane, as a model for the reaction of heme with artemisinin. A comparison is made with the reaction of dihydrated ferrous hydroxide with O(2), as a model for the heme interaction with oxygen. We found that dihydrated Fe(OH)(2) reacts more efficiently with the artemisinin model than with O(2). This result suggests that artemisinin instead of molecular oxygen would interact with heme, disrupting its detoxification process by avoiding the initial heme to hemin oxidation, and killing in this way the malaria parasite. The ELF and AIM theories provide support for such a conclusion, which further clarifies our understanding on how artemisinin acts as an antimalarial agent.

Structural reassignment, absolute configuration, and conformation of hypurticin, a highly flexible polyacyloxy-6-heptenyl-5,6-dihydro-2H-pyran-2-one

The structural reassignment, absolute configuration, and conformational behavior of the highly flexible natural product hypurticin (pectinolide E), 6S-[3'S,5'R,6'S-triacetoxy-1Z-heptenyl]-5S-acetoxy-5,6-dihydro-2H-pyran-2-one (1), were ascertained by a molecular modeling protocol, which includes extensive conformational searching, geometry optimization by DFT B3LYP/DGDZVP calculations, and comparison between the theoretical (DFT) and experimental (1)H-(1)H NMR coupling constants. Hyptolide (2), a related cytotoxic 5,6-dihydro-2H-pyran-2-one that increased the S phase of the HeLa cell cycle, was employed as a reference substance to validate the theoretical protocol designed to characterize the 3D properties of compound 1. The related synthetic derivative, tri-O-acetyl-3,6-dideoxy-d-glucose diphenyldithioacetal (14), was prepared by a six-step reaction sequence starting from d-glucose and served as an enantiopure building block to reinforce the structural and configurational assignment of 1. This protocol proved to be an important tool for the structural characterization of highly flexible bioactive polyoxygenated natural products.

Dissociative Electron Attachment to Di-tert-butylperoxide, Artemisinin, and β-Artemether

The gas-phase dissociative electron attachment spectra of di-tert-butylperoxide (DBP) and the antimalarial polycyclic peroxides artemisinin and beta-artemether are presented for the first time. The total anion currents measured at the walls of the collision chamber and the mass selected anion currents are reported in the 0-6 eV energy range. Electron attachment to DBP produces an intense current, peaking at 1.3 eV, due to the C4H9O- negative fragment, in line with the strongly O-O antibonding character of the singly occupied orbital of the parent molecular anion and the small (if any) thermodynamic energy threshold predicted by B3LYP calculations for the formation of this anion fragment. A five times less intense signal, with m/e = 57 and a maximum at 0.7 eV, is also observed. The calculations exclude that this signal can be associated with the C4H9- negative fragment, whereas they support its assignment to the C3H5O- species, generated by simultaneous dissociation and loss of a methane molecule from the parent molecular anion. In DBP, artemisinin, and beta-artemether, currents corresponding to the parent molecular anion are not detected, indicating that its survival time is shorter than the time required (about 10-6 s) to pass through the mass filter. In the latter two compounds, where simple O-O bond breaking does not generate separate fragments, the anion currents are much weaker than in DBP and the maximum total anion current peaks at zero energy.