1,720,997 research outputs found
On the interplay among non-covalent interactions and activity of 4-aminoquinoline antimalarials: a crystallographic and spectroscopic study
Full text linkMalaria is due to protozoa of the genus Plasmodium, which infect human red blood cells and digest the host hemoglobin. Degradation of the latter in the acidic food vacuole (pH ~ 5) releases free hematin (hydroxylated Fe protoporphyrin-IX, FePPIX(OH)), which is toxic to the parasite [1]. Therefore, Plasmodium deactivates hematin by promoting its crystallization into harmless pale yellow P1bar crystals of beta-hematin. 4-aminoquinoline drugs (AQ), such as chloroquine (CQ) and piperaquine (PQ), interfere with this detoxification process, either by coordinating free heme in solution [2], or by poisoning fastest-growing crystal faces of beta-hematin [3]. However, there is no general consensus on the structure of the AQ/heme complex [4], which depends on various chemical variables (aqueous/lipidic environment, pH).
We here aim at quantitatively disclosing the chemical physics underlying the pharmacophoric features of CQ and PQ in the context of predicting which chemical modifications should be applied on the AQ scaffold to enhance the drug functionality against the biochemical resistance mechanism evolved by Plasmodium [5,6].
EXAFS spectroscopy in solution across the Fe Kalpha absorption edge (~ 7.1 keV) explored the first shell coordination geometry of iron in hematin, both in the presence and in the absence of AQ systems. Differences in the signal were related to the possible occurrence of a direct Fe–N coordinative bond involving the quinoline nitrogen atom, which might coexist with other possible (e.g. pi···pi stacked) adduct geometries [5] (Fig. 1). Quantum mechanical DFT calculations showed that an aliphatic tertiary NH+ amino group might also be a crucial part of the pharmacophore (Fig. 1), as it is able to set up strong charge-assisted hydrogen bonds with proprionate groups of hematin. This complies well with single-crystal X-ray diffraction outcomes on the CQ dihydrogen phosphate salt at 103 K[6], where H2PO4– ions form hydrogen-bonded pillars which strongly interact with positively charged chloroquine molecules. Comparison of the CQ crystal structure with those of various hydrated salts of PQ (NO3–, SO42–, H2PO4–), grown by advanced sol-gel methods, disclosed subtle analogies and differences in the non-covalent interaction networks of the two drugs, which are also related to their solubilities.
[1] L. Kořený, M. Oborník, J. Lukeš, PLoS Pathog. 2013, 9(1), e1003088.
[2] D.C. Warhurst J.C. Craig, K.S. Raheem, Biochem. Pharmacol. 2007, 73, 1910.
[3] M.S.Walczak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A.J. Kosar, D.S. Bohle J. Phys. Chem. B 2011, 115, 1145.
[4] J. Gildenhuys, T. Roex, T.J. Egan, K.A. De Villiers, J. Am. Chem. Soc. 2013, 135, 1037.
[5] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini, L. Lo Presti, Physica Scripta 2016, 91, 023001.
[6] G. Macetti, L. Loconte, S. Rizzato, C. Gatti, L. Lo Presti, Crystal Growth Des. 2016. 16, 6043
Pre-nucleation clusters in liquid benzoic acid
Full text linkCarboxylic acids play a pivotal role in crystal engineering, owing to their ability to form hydrogen-bonded cyclic dimers, which route the crystallization process. Benzoic acid (BZA) is the prototype of aromatic carboxylic acids. Recent results from our group point out that several intermolecular recognition modes are present in the liquid phase, where the cyclic dimers that are found also in the P21/c crystal – the only known to date – are overcome by trimeric structures with almost trigonal symmetry, and coexist with greater and more complex HB clusters. Thus, a question arises – when and why does the structure of the liquid change, so that nucleation of BZA dimers can occur? To gain insights on the problem, we investigate liquid benzoic acid as a function of T by means of molecular dynamics with the free MiCMoS platform. We propose novel structure-free energy-based criteria to highlight relevant supramolecular clusters that show a detectable cohesion and, for this reason, have lifetimes significantly longer than thermal fluctuations. Our tool allows to single out nanoscale inhomogeneities that impact on the average structure of the liquid, in what is the nano-equivalent of bulk de-mixing within a binary system. We find clusters up to 17 molecules large that persist by more than 100 ps in undercooled BZA, and display an inner structure that is somewhat intermediate between the liquid and the crystal. Thus, they might lie on the path to the ripening of critical clusters or semi-liquid crystal embryos. Large aggregates still lack a definite inner symmetry and are highly dynamic and fluxional, as we expect. We hypothesise that, on longer time scales, persistent nanoscale inhomogeneities could set up a favourable environment that enhances the probability of nucleation, in agreement with non-classical theories
Experimental and theoretical study of the mechanism of action of the antimalarial drug chloroquine
Full text linkMalaria is due to the Plasmodium protozoon. The parasite infects human red blood cells, where it digests hemoglobin, in the end releasing free heme (Fe-protoporphyrin IX, FePPIX) in the cytosol. There, FePPIX could produce reactive oxygen species which are toxic to the parasite.
As a defense mechanism, the protozoon deactivates FePPIX by promoting its biocrystallization into hemozoin, a triclinic harmless solid. It is largely accepted that 4-aminoquinoline (AQ) drugs, and in particular the low-cost compound chloroquine (CQ), interfere with this detoxification process [1], but no unequivocal evidences on their mechanism of action still exist [2,3]. Moreover, emerging parasite resistance made CQ ineffective in the last decades. In this context, understanding the mechanism of action of chloroquine is a key point to develop novel cheap CQ-based compounds, exploitable in large-scale health campaigns, able to thwart the parasite resistance.
In our very recent work [4], evidences of the existence of a direct Fe – N coordinative bond between CQ and heme in solution have been obtained. DFT calculations highlighted that charge-assisted hydrogen bonds (CAHBs) among the hydrocarbon chain of CQ and the propionate groups of heme play a crucial role in the molecular recognition, particularly in the presence of lipidic micelles.
In this contribution we report on a high-resolution low-temperature single crystal X-ray diffraction study on the chloroquine diphosphate dihydrate salt. CQ crystallizes as P21/c, with dihydrogenphosphate ions (H2PO4–) forming infinite chains parallel to the monoclinic axis. Doubly protonated CQ molecules, CQH22+, and H2PO4– are connected through strong N-H•••O CAHBs. A π-π stacking interaction could be also set up between the quinoline rings, which lie parallel to the (a,c) plane to occupy as much as possible the free space between phosphate chains.
From the molecular recognition viewpoint, π-π stacking in the CQ crystal could be taken as a model for the π-π CQ:heme interaction in solution, described in the literature as a possible way of interaction between the drug and its substrate, while negatively charged the phosphate ions behave as propionate groups in heme.
The study of the CQ self-recognition energies through the analysis of the primary charge density confirm the hypothesis that the coulombic interactions between CQ and the phosphate are the real dominant ones, while the stacking between the quinoline moieties has just an ancillary role. These evidences further confirm that the protonated tertiary amine of CQ is an essential component of the drug pharmacophore.
[1] A. F. G. Slater, W. J. Swiggard, B. R. Orton, W. D. Flitter, D. E. Goldberg. A. Cerami, G. B. Henderson Proc. Natl. Acad. Sci. USA 1991, 88, 325-329.
[2] M. S. Walckzak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A. J. Kosar, D. S. Bohle J. Phys. Chem. B, 2011, 115, 1145-1150.
[3] A. C. De Dios, R. Tycko, L. M. B. Ursos, P. D. Roepe J. Phys. Chem. A, 2003, 107, 5821-5825.
[4] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini, L. Lo Presti Physica Scripta 2016, 91, 023001, 1-13
Subcritical clusters of liquid benzoic acid: insights from molecular dynamics simulations
Full text linkNucleation is a crucial process in material science and pharmaceutical chemistry, yet it remains poorly understood and presents numerous unanswered questions. How does a crystal nucleus form? Does it emerge from a completely disordered liquid phase through the continuous addition of building units, as suggested by Classical Nucleation Theory? And is the structure of the nucleus identical to that of the resulting crystal? Recent studies, suggest that for benzoic acid, nucleation may occur via a non-classical pathway. This is due to the formation of stable aggregates in the liquid phase, which persist for several picoseconds but do not share the same structure as the final crystal. However, a precise and unique definition of these so-called subcritical clusters is elusive, due to their dynamic nature. In this work, we perform molecular dynamics simulations on liquid benzoic acid employing the free MiCMoS platform, and propose a definition of subcritical clusters based on three criteria: molecular connectivity, time persistence, and energetic stability. Finally, we describe the structural and dynamic characteristics of subcritical clusters comparing them with the crystallographic structure. Subcritical clusters must be aggregates of bonded molecules: two molecules are considered bonded if their interaction energy is more negative than a specified energy threshold. Additionally, these aggregates must be persistent, meaning that their lifetime must exceed that of thermal fluctuations. Furthermore, they must be energetically "stable": we introduce the concept of excess energy as a stability condition, defined as the difference between the cohesive energy of the aggregate and the interaction energy between the aggregate and the surrounding molecules. Only aggregates meeting all these criteria are considered subcritical clusters: they must exhibit interaction energies more negative than an arbitrary “binding” threshold, lifetimes longer than thermal fluctuations, and a negative average excess energy. Interestingly, while the P21/c crystal structure of benzoic acid consists of cyclic dimers, the subcritical clusters are composed of folded H-bonded catemers with a globular shape. Longer simulations and a systematic study of their temporal evolution could potentially reveal the growth of these subcritical clusters and their eventual rearrangement into a crystal nucleus
Study of the key interactions in the self-recognition of the antimalarial drug chloroquine
Full text linkMalaria is a parasitic disease that causes thousands of deaths every year, especially in undeveloped countries. The Plasmodium protozoa, responsible of the infection, kill human red blood cells by digesting hemoglobin. Many compounds have been employed in the last century against malaria, but nowadays the increasing resistance of Plasmodium is becoming a very serious problem. New drugs are required and to this end it is desirable to quantitatively understand the role of different functional groups in determining effective pharmacophores.
This work focuses on chloroquine (CQ), a 4-aminoquinoline antiplasmodial whose effectiveness is now hampered by evolved parasite resistance. It is accepted that CQ interferes with a crucial detoxification process of the parasite [1], namely the inhibition of heme bio-crystallization, but several details of this process still remain rather obscure. In the acidic digestive vacuole of Plasmodium, CQ is supposed to interact in its diprotonated form directly with the monomeric heme in two possible ways: 1) π-π stacking interactions between quinoline ring and heme proto-porphyrin [2] or 2) a direct Fe-N quinoline coordinative bond, supported by strong charge-assisted hydrogen bonds (CAHBs) between the tertiary amine of CQ and the propionate groups of heme [3-4].
In this work, the self-recognition of chloroquine diphosphate dihydrate salt was studied both theoretically and experimentally. High-resolution single crystal X-ray data were collected at low temperature (103 K) and complemented by quantum simulations with CRYSTAL14 [5] at the B3LYP/6-31G(p,d) theory level. The salt crystalizes in a P21/c structure, with phosphate ions forming infinite chains parallel to the b axis. CQ molecules and phosphates are connected through strong N-H•••O CAHBs, while a π-π interaction is present between the quinoline rings (see figure).
The topological analysis of the primary charge density, performed according with the Quantum Theory of Atoms in Molecules [6], along with the ab-initio energy decomposition, show that the coulombic interactions between the charged hydrocarbon chain of CQ and the phosphate ions seem to provide the dominant features in the molecular self-recognition, while the π-π stacking between the quinoline moieties has just an ancillary role. These evidences suggest that, in agreement with our previous DFT/EXAFS results [3], the protonated tertiary amine of CQ is an essential component of the drug pharmacophore.
[1] A. F. G. Slater, W. J. Swiggard, B. R. Orton, W. D. Flitter, D. E. Goldberg. A. Cerami and G. B. Henderson, Proc. Natl. Acad. Sci. USA 1991, 88, 325
[2] M. S. Walckzak, K. Lawniczak-Jablonska, A. Wolska, A. Sienkiewicz, L. Suarez, A. J. Kosar and D. S. Bohle, J. Phys. Chem. B 2011, 115, 1145
[3] G. Macetti, S. Rizzato, F. Beghi, L. Silvestrini and L. Lo Presti, Physica Scripta 2016, 91, 023001
[4] A. C. De Dios, R. Tycko, L. M. B. Ursos and P. D. Roepe, J. Phys. Chem. A 2003, 107, 5821
[5] R. Dovesi, V. R. Saunders, C. Roetti, R. Orlando, C. M. Zicovich-Wilson, F. Pascale, B. Civalleri, K. Doll, N. M. Harrison, I. J. Bush, P. D’Arco, M. Llunell, M. Causà and Y. Noël, CRYSTAL14 2014 CRYSTAL14 User's Manual. University of Torino, Torino
[6] R. F. W. Bader, Atoms in molecules. A quantum theory 1990, Oxford University Press. Oxford, U.K
Unveiling interactions of the antimalarial drug chloroquine with haeme in aqueous solutions through spectroscopic and quantum mechanical methods
No full textMalaria is one of the most worldwide spread parasitic disease. It is caused by Plasmodium protozoa, which eventually infect human erythrocytes and digest the host haemoglobin. This process releases free haeme (Fe-protoporphyrin-IX), which is toxic to the parasite as it produces reactive oxygen species (ROS), the cause of oxidative stress. The protozoon deactivates haeme by promoting its crystallization into solid pale-yellow hemozoin, that gives the characteristic skin color of malaria-infected people. Aminoquinoline-type (AQ) drugs interfere with this detoxification process either by directly hampering haeme- haeme self-recognition in solution [1] or by preventing the growth of hemozoin crystals [2] (Figure 1). The nature of the specific AQ compound-haeme scaffold interactions is not yet understood, even though it is a necessary requirement to explicate antiplasmodial activity. We report here on an experimental and theoretical study of the AQ- type antimalarial chloroquine (CQ)-free haeme interactions in aqueous solutions. Extended X-ray Absorption Fine Structure (EXAFS) experiments at the Fe Kα absorption edge (7.1 keV) were performed at the BM26A station of the ESRF facility in Grenoble (FR) on various haeme-containing solutions, both in the presence and in the absence of CQ. The effect of pH was monitored through the addition of suitable buffers in the 4–7 range at variable pH interval. A tensioactive (sodium dodecyl sulfate) at its critical micellar concentration was also employed to model lipidic nanodroplets in the parasite food vacuole, as their presence was reported [3] to favor hemozoin crystallization (Figure 1). EXAFS results were complemented by accurate UV absorption measurements of the same solutions and DFT B3LYP 6-311G(d,p) simulations of possible haeme:chloroquine adduct geometries. We found evidence that, at least in the experimental conditions here employed, CQ does not set stacking π···π interactions with the protoporphyrin scaffold, even though this geometry was proposed as the most probable one through molecular mechanics simulations [4,5] and previous EXAFS studies of mesohaematin anhydride in dimethylsulfoxyde [6]. Rather, our DFT calculations point out that CQ and haeme seem to recognize each other through electrostatic interactions among lateral charged groups. If proven true, this would have obvious implications on the engineering of novel antimalarials able to thwart the parasite adaptability against classical AQ-based therapies. Acknowledgments: This work has been supported by Unimi Development Plan – Line B1 and CINECA – [1] Slater et al., Proc. Natl. Acad. Sci. USA 1991, 88, 2, [2] Gildenhuys et al., J. Am. Chem. Soc. 2013, 135, 3, [3] Pisciotta et al. Biochem. J., 2007, 402, 1, 197. [6] Walczac et al., J. Phys. Chem. B, 2011, 115, 5, 11 [4] Warhurst et al, Biochem. Pharmacol. 2007, 73, 12, 1910. [5] Otelo et al., Bioorganic & Medicinal Chemistry Letters 2011, 21, 1, 250
Insights on spin delocalization and spin polarization mechanisms in crystals of azido copper(II) dinuclear complexes through the electron spin density Source Function
Full text linkThe Source Function (SF) tool was applied to the analysis of the theoretical spin density in azido CuII dinuclear complexes, where the azido group, acting as a coupler between the CuII cations, is linked to the metal centres either in an end-on or in an end-end fashion. Results for only the former structural arrangement are reported in the present paper. The SF highlights to which extent the magnetic centres contribute to determine the local spin delocalization and polarization at any point in the dimetallic complex and whether an atom or group of atoms of the ligands act in favour or against a given local spin delocalization/polarization. Ball-and-stick atomic SF percentage representations allow for a visualization of the magnetic pathways and of the specific role played by each atom along these paths, at given reference points. Decomposition of SF contributions in terms of a magnetic and of a relaxation component provides further insight. Reconstruction of partial spin densities by means of the Source Function has for the first time been introduced. At variance with the standard SF percentage representations, such reconstructions offer a simultaneous view of the sources originating from specific subsets of contributing atoms, in a selected molecular plane or in the whole space, and are therefore particularly informative. The SF tool is also used to evaluate the accuracy of the analysed spin densities. It is found that those obtained at the unrestricted B3LYP DFT level, relative to those computed at the CASSCF(6,6) level, greatly overestimate spin delocalization to the ligands, but comparatively underestimate magnetic connection (spin transmission) among atoms, along the magnetic pathways. As a consequence of its excessive spin delocalization, the UB3LYP method also overestimates spin polarization mechanisms between the paramagnetic centres and the ligands. Spin delocalization measures derived from the refinement of Polarized Neutron Diffraction data seem in general superior to those obtained through the DFT UB3LYP approach and closer to the far more accurate CASSCF results. It is also shown that a visual agreement on the spin-resolved electron densities rho(alpha) and rho(beta) derived from different approaches does not warrant a corresponding agreement between their associated spin densities.Electron spin density at a point may be seen as determined by a local Source Function for such density, operating at all other points of space. Integration of the local source over Bader's quantum atoms measures their contribution in determining the spin density features at any system's location. This novel tool is able to provide interesting insights on the electron spin delocalization and polarization mechanisms along with their dependence from the spin density quality
On the molecular basis of the activity of the antimalarial drug chloroquine : EXAFS-assisted DFT evidence of a direct Fe–N bond with free heme in solution
Full text link4-aminoquinoline antiplasmodials interfere with the biocrystallization of the malaria pigment, a key step of the malaria parasite metabolism. It is commonly believed that these drugs set stacking π ··· π interactions with the Fe-protoporphyrin scaffold of the free heme, even though the details of the heme:drug recognition process remain elusive. In this work, the local coordination of Fe(III) ions in acidic solutions of hematin at room temperature was investigated by extended x-ray absorption fine structure (EXAFS) spectroscopy in the 4.0–5.5 pH range, both in the presence and in the absence of the antimalarial drug chloroquine. EXAFS results were complemented by DFT simulations in polarizable continuum media to model solvent effects. We found evidence that a complex where the drug quinoline nitrogen is coordinated with the iron center might coexist with formerly proposed adduct geometries, based on stacking interactions. Charge-assisted hydrogen bonds among lateral chains of the two molecules play a crucial role in stabilizing this complex, whose formation is favored by the presence of lipid micelles. The direct Fe–N bond could reversibly block the axial position in the Fe 1st coordination shell in free heme, acting as an inhibitor for the crystallization of the malaria pigment without permanently hampering the catalytic activity of the redox center. These findings are discussed in the light of possible implications on the engineering of drugs able to thwart the adaptability of the malaria parasite against classical aminoquinoline-based therapies
Understanding self-recognition in the antimalarial drug chloroquine: an experimental and theoretical charge density study
No full textMalaria is the topmost world parasitic disease, with hundred of thousand deaths for year, most of which drug. In this context, the present work focuses on the experimental and theoretical characterization of chemical bonds and intermolecular interactions in crystalline CQ [1]. Chloroquine diphosphate salt was crystallized by various methods, including sol-gel techniques. Single-crystal X-Ray data collections were performed among room temperature (RT) and 100 K, using a Mo Ka source. CQ is a di-cation with protonated basic functions on quinolone. In the solid-state, complex patterns of hydrogen bonds (HBs) involving both the phosphate groups and co-crystallized water molecules are set up. Phosphate ions form infinite chains parallel to the monoclinic b axis, while CQ molecules keep their fused ring system orthogonal to the chains (see the Figure), setting in the free space among them through allegedly strong N–H···O HBs. The role of the two water molecules is less clear, even though they should help to coordinate phosphate ions. Even at 100 K, the X-ray data were not able to unequivocally determine the exact position of the H atoms. We therefore complemented the X-ray model by solid-state DFT simulations, but at least one water hydrogen has no obvious close acceptors and some kind of disorder cannot be excluded. On the basis of the solid-state DFT model, we applied the Hansen-Coppens multipolar approach [2] to study the experimental charge density in CQ diphosphate. The effect of the crystal field on the molecular conformation and the self-recognition energetics were investigated by both topological and quantum mechanical approaches. The importance of different intermolecular interaction patterns in setting up a stable crystal field is discussed. Acknowledgments: G. Macetti gratefully acknowledges travel support by AIC (Italian Crystallographic Association). This work has been supported by Unimi Development Plan – Line B1 and CINECA – ISCRA C (QUADRUG).
[1] Karle et al. Acta Crystallogr . 1988, C44, 1605.
[2] Hansen et al. Acta Crystallogr. 1978, A34, 90
- …
