Toward Understanding the Chloroquine Action at the Molecular Level in Antimalarial Therapy − X-ray Absorption Studies in Acetic Acid Solution

Soluble meso and deuteroporphyrin analogs of the malaria pigment hematin anhydride

Two soluble heme analogs of the insoluble malaria pigment hematin anhydride (HA, or β-hematin), [Fe(III)(protoporphyrin)]2, with either mesoporphyrin (MHA) or deuteroporphyrin (DHA) are characterized by elemental analysis, SEM, IR spectroscopy, electronic spectroscopy, paramagnetic 1H NMR spectroscopy and solution magnetic susceptibility. While prior single crystal and X-ray powder diffraction results indicate all three have a common propionate linked dimer motif, there is considerable solid state variation in the conformation. This is associated with enhanced solubility of MHA and DHA. As with HA, DHA undergoes thermally promoted reversible hydration/dehydration in the solid state. Solution 1H NMR studies of DHA suggest a high spin dimeric structure with the porphyrin methyls distributed between two isomers which are also present in the solid state. These soluble iron(III)porphyrin dimers allow for the first direct solution studies by NMR and UV-Vis spectroscopies of these key species. Taken together the results illustrate the importance and utility of varying the substituents on the periphery of the porphyrin for studying heme aggregation and malaria pigment formation.

Computational insights into the inhibition of β-haematin crystallization by antimalarial drugs

During the red blood cell phase of their life cycle, malaria parasites digest their host's haemoglobin, with concomitant release of potentially toxic iron(iii) protoporphyrin IX (FePPIX). The parasites' strategy for detoxification of FePPIX involves its crystallization to haemozoin, such that the build-up of free haem in solution is avoided. Antimalarial drugs of both historical importance and current clinical use are known to be capable of disrupting the growth of crystals of β-haematin, which is the synthetic equivalent of haemozoin. Hence, the disruption of haemozoin crystal growth is implicated as a possible mode of action of such drugs. However, the details of β-haematin crystal poisoning at the molecular level have yet to be fully elucidated. In this study, we have used a combination of density functional theory (DFT) and molecular modelling to examine the possible modes of action of ten different antimalarial drugs, including quinine-type aliphatic alcohols, amodiaquine-type phenols, and chloroquine-type aliphatic diamines. The DFT calculations indicate that each of the drugs can form at least one molecular complex with FePPIX. These complexes have 1 : 1 or 2 : 1 FePPIX : drug stoichiometries and all of them incorporate Fe-O bonds, formed either by direct coordination of a zwitterionic form of the drug, or by deprotonation of water. Most of the drugs can form more than one such complex. We have used the DFT model structures to explore the possible formation of a monolayer of each drug-haem complex on four of the β-haematin crystal faces. In all cases, the drug complexes can form a monolayer on the fast-growing {001} and {011} faces, but not on the slower growing {010} and {100} faces. Additional modelling of the chloroquine and quinidine complexes shows that individual molecules of these species can also obstruct the growth of new layers on other crystal faces. The implications of these observations for antimalarial drug development are discussed.

Alkoxide coordination of iron(III) protoporphyrin IX by antimalarial quinoline methanols: a key interaction observed in the solid-state and solution

The quinoline methanol antimalarial drug mefloquine is a structural analogue of the Cinchona alkaloids, quinine and quinidine. We have elucidated the single crystal X-ray diffraction structure of the complexes formed between racemic erythro mefloquine and ferriprotoporphyrin IX (Fe(iii)PPIX) and show that alkoxide coordination is a key interaction in the solid-state. Mass spectrometry confirms the existence of coordination complexes of quinine, quinidine and mefloquine to Fe(iii)PPIX in acetonitrile. The length of the iron(iii)-O bond in the quinine and quinidine complexes as determined by Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy unequivocally confirms that coordination of the quinoline methanol compounds to Fe(iii)PPIX occurs in non-aqueous aprotic solution via their benzylic alkoxide functional group. UV-visible spectrophotometric titrations of the low-spin bis-pyridyl-Fe(iii)PPIX complex with each of the quinoline methanol compounds results in the displacement of a single pyridine molecule and subsequent formation of a six-coordinate pyridine-Fe(iii)PPIX-drug complex. We propose that formation of the drug-Fe(iii)PPIX coordination complexes is favoured in a non-aqueous environment, such as that found in lipid bodies or membranes in the malaria parasite, and that their existence may contribute to the mechanism of haemozoin inhibition or other toxicity effects that lead ultimately to parasite death. In either case, coordination is a key interaction to be considered in the design of novel antimalarial drug candidates.

Solution structures of chloroquine-ferriheme complexes modeled using MD simulation and investigated by EXAFS spectroscopy

The interaction of chloroquine (CQ) and the μ-oxo dimer of iron(III) protoporphyrin IX (ferriheme) in aqueous solution was modeled using molecular dynamics (MD) simulations. Two models of the CQ-(μ-oxo ferriheme) complex were investigated, one involving CQ π-stacked with an unligated porphyrin face of μ-oxo ferriheme and the other in which CQ was docked between the two porphyrin rings. The feasibility of both models was tested by fitting computed structures to the experimental extended X-ray absorption fine structure (EXAFS) spectrum of the CQ-(μ-oxo ferriheme) complex in frozen aqueous solution. The docked model produced better agreement with experimental data, suggesting that this is the more likely structure in aqueous solution. The EXAFS fit indicated a longer than expected Fe-O bond of 1.87Å, accounting for the higher than expected magnetic moment of the complex. As a consequence, the asymmetric Fe-O-Fe stretch shifts much lower in frequency and was identified in the precipitated solid at 744cm(-1) with the aid of the O(18) isomer shift. Three important CQ-ferriheme interactions were identified in the docked structure. These were a hydrogen bond between the oxide bridge of μ-oxo ferriheme and the protonated quinolinium nitrogen atom of CQ; π-stacking between the quinoline ring of CQ and the porphyrin rings; and a close contact between the 7-chloro substituent of CQ and the porphyrin methyl hydrogen atoms. These interactions can be used to rationalize previously observed structure-activity relationships for quinoline-ferriheme association.

X-ray techniques for innovation in industry

The smart specialization declared in the European program Horizon 2020, and the increasing cooperation between research and development found in companies and researchers at universities and research institutions have created a new paradigm where many calls for proposals require participation and funding from public and private entities. This has created a unique opportunity for large-scale facilities, such as synchrotron research laboratories, to participate in and support applied research programs. Scientific staff at synchrotron facilities have developed many advanced tools that make optimal use of the characteristics of the light generated by the storage ring. These tools have been exceptionally valuable for materials characterization including X-ray absorption spectroscopy, diffraction, tomography and scattering, and have been key in solving many research and development issues. Progress in optics and detectors, as well as a large effort put into the improvement of data analysis codes, have resulted in the development of reliable and reproducible procedures for materials characterization. Research with photons has contributed to the development of a wide variety of products such as plastics, cosmetics, chemicals, building materials, packaging materials and pharma. In this review, a few examples are highlighted of successful cooperation leading to solutions of a variety of industrial technological problems which have been exploited by industry including lessons learned from the Science Link project, supported by the European Commission, as a new approach to increase the number of commercial users at large-scale research infrastructures.

Molecular structures and solvation of free monomeric and dimeric ferriheme in aqueous solution: insights from molecular dynamics simulations and extended X-ray absorption fine structure spectroscopy

CHARMM force field parameters have been developed to model nonprotein bound five-coordinate ferriheme (ferriprotoporphyrin IX) species in aqueous solution. Structures and solvation were determined from molecular dynamics (MD) simulations at 298 K of monomeric [HO-ferriheme](2-), [H2O-ferriheme](-), and [H2O-ferriheme](0); π-π dimeric [(HO-ferriheme)2](4-), [(H2O-ferriheme)(HO-ferriheme)](3-), [(H2O-ferriheme)2](2-), and [(H2O-ferriheme)2](0); and μ-oxo dimeric [μ-(ferriheme)2O](4-). Solvation of monomeric species predominated around the axial ligand, meso-hydrogen atoms of the porphyrin ring (Hmeso), and the unligated face. Existence of π-π ferriheme dimers in aqueous solution was supported by MD calculations where such dimers remained associated over the course of the simulation. Porphyrin rings were essentially coplanar. In these dimers major and minor solvation was observed around the axial ligand and Hmeso positions, respectively. In μ-oxo ferriheme, strong solvation of the unligated face and bridging oxide ligand was observed. The solution structure of the μ-oxo dimer was investigated using extended X-ray absorption fine structure (EXAFS) spectroscopy. The EXAFS spectrum obtained from frozen solution was markedly different from that recorded on dried μ-oxo ferriheme solid. Inclusion of five solvent molecules obtained from spatial distribution functions in the structure generated from MD simulation was required to produce acceptable fits to the EXAFS spectra of the dimer in solution, while the solid was suitably fitted using the crystal structure of μ-oxo ferriheme dimethyl ester which included no solvent molecules.

A computational study of ligand binding affinities in iron(iii) porphine and protoporphyrin IX complexes

In the context of antimalarial drug development, density functional theory has been used to model the interactions between a diverse set of 31 small ligands and the iron(iii) centre of ferriprotoporphyrin IX, as well as key events in the crystallization of this molecule by the malaria parasite.

Synchrotron Radiation Spectroscopic Techniques as Tools for the Medicinal Chemist: Microprobe X-Ray Fluorescence Imaging, X-Ray Absorption Spectroscopy, and Infrared Microspectroscopy

This review updates the recent advances and applications of three prominent synchrotron radiation techniques, microprobe X-ray fluorescence spectroscopy/imaging, X-ray absorption spectroscopy, and infrared microspectroscopy, and highlights how these tools are useful to the medicinal chemist. A brief description of the principles of the techniques is given with emphasis on the advantages of using synchrotron radiation-based instrumentation rather than instruments using typical laboratory radiation sources. This review focuses on several recent applications of these techniques to solve inorganic medicinal chemistry problems, focusing on studies of cellular uptake, distribution, and biotransformation of established and potential therapeutic agents. The importance of using these synchrotron-based techniques to assist the development of, or validate the chemistry behind, drug design is discussed.