π-Stacked polyphenolic dimers: A case study using dispersion-corrected methods

The accuracy of dispersion-corrected calculations (DFT-D2, DFT-D3 and DFT-NL) is assessed here, with large basis sets (def2-QZVP) to avoid incompleteness effects, for the most stable structure of a real-world polyphenol dimer chosen as an appropriate model. Natural polyphenols form such complexes with π-stacking playing a key stabilizing role. Our benchmark calculations predict its existence favored by 22–24 kcal/mol with respect to the isolated monomers, mainly driven by both π–π and H-bonding interactions. The adequate comparison of lower-cost DFT-based methods allowed bracketing their expected accuracy. These results thus pave the way towards reliable studies of challenging aggregation processes of natural products.The work in Alicante is supported by the ‘Ministerio de Educación y Ciencia’ of Spain and the ‘European Regional Development Fund’ through project CTQ2011-27253. The work in Mons is supported by the Belgian National Fund for Scientific Research (FNRS). The work in Limoges is supported by the ‘Conseil Régional du Limousin’ and COST actions FA1003 ‘East–West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding’ and CM0804 ‘Chemical Biology with Natural Products’. The work in Malaysia is supported by Akademi Sains Malaysia through the SAGA Grant C20 and by the Ministry of Higher Education through the Grant 600-RMI/ST/FRGS 5/3/Fst (4/2011). The authors gratefully acknowledge the support by the Operational Program Research and Development for Innovation–European Regional Development Fund (Project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic). I.B. gratefully thanks the ‘Association Djerbienne de France’ (ADF) for the financial support

Bottom-up hierarchical self-assembly of chiral porphyrins through coordination and hydrogen bonds

A series of chiral synthetic compounds is reported that show intricate but specific hierarchical assembly because of varying positions of coordination and hydrogen bonds. The evolution of the aggregates (followed by absorption spectroscopy and temperature-dependent circular dichroism studies in solution) reveal the influence of the proportion of stereogenic centers in the side groups connected to the chromophore ring in their optical activity and the important role of pyridyl groups in the self-assembly of these chiral macrocycles. The optical activity spans two orders of magnitude depending on composition and constitution. Two of the aggregates show very high optical activity even though the isolated chromophores barely give a circular dichroism signal. Molecular modeling of the aggregates, starting from the pyridine-zinc(II) porphyrin interaction and working up, and calculation of the circular dichroism signal confirm the origin of this optical activity as the chiral supramolecular organization of the molecules. The aggregates show a broad absorption range, between approximately 390 and 475 nm for the transitions associated with the Soret region alone, that spans wavelengths far more than the isolated chromophore. The supramolecular assemblies of the metalloporphyrins in solution were deposited onto highly oriented pyrolitic graphite in order to study their hierarchy in assembly by atomic force microscopy. Zero and one-dimensional aggregates were observed, and a clear dependence on deposition temperature was shown, indicating that the hierarchical assembly took place largely in solution. Moreover, scanning electron microscopy images of porphyrins and metalloporphyrins precipitated under out-of-equilibrium conditions showed the dependence of the number and position of chiral amide groups in the formation of a fibrillar nanomaterial. The combination of coordination and hydrogen bonding in the complicated assembly of these molecules - where there is a clear hierarchy for zinc(II)-pyridyl interaction followed by hydrogen-bonding between amide groups, and then van der Waals interactions - paves the way for the preparation of molecular materials with multiple chromophore environments

Optical properties of wine pigments: theoretical guidelines with new methodological perspectives

Wine pigmentation results from the complex chemistry of anthocyanins. Their flavylium cation form is stabilized either by chemical transformation occurring during wine aging (e.g., pyranoanthocyanin formation), or by the formation of non-covalent complexes with (phenolic) copigments. Molecular modeling (quantum mechanics and molecular dynamics) is more and more adapted to understand wine chemistry and pigmentation. The constant developments of theoretical methodologies might get non-specialists easily lost. This manuscript is a review of the theoretical studies dedicated to the field of wine pigments, showing conformational analysis, energetics of the various forms, pigment/copigment (non-)covalent association, and charge transfer excited states. QM/MM calculations are newly performed here, which improve solvent description. The conclusion is a comprehensive guideline for an accurate prediction of light absorption by wine pigments and all related supramolecular processes.P.T. thanks INSERM and the ‘Conseil Régional du Limousin’. Financial support from the Czech Science Foundation (P208/12/G016), the Operational Program Research and Development for Innovations—European Regional Development Fund (project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic), the Barrande Project (No. 7AMB12FR026) and the Operational Program Education for Competitiveness—European Social Fund (project CZ.1.07/2.3.00/20.0058 of the Ministry of Education, Youth and Sports of the Czech Republic) is also gratefully acknowledged. The work at IMDEA was supported by the Spanish Ministerio de Economía y Competitividad (MINECO; project CTQ2011-27317). M.L. thanks the Swedish e-Science Research Center (SeRC) for financial support

Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes

The human SLC22A6/OAT1 plays an important role in the elimination of a broad range of endogenous substances and xenobiotics thus attracting attention from the pharmacological community. Furthermore, OAT1 is also involved in key physiological events such as the remote inter-organ communication. Despite its significance, the knowledge about hOAT1 structure and the transport mechanism at the atomic level remains fragmented owing to the lack of resolved structures. By means of protein-threading modeling refined by μs-scaled Molecular Dynamics simulations, the present study provides the first robust model of hOAT1 in outward-facing conformation. Taking advantage of the AlphaFold 2 predicted structure of hOAT1 in inward-facing conformation, we here provide the essential structural and functional features comparing both states. The intracellular motifs conserved among Major Facilitator Superfamily members create a so-called “charge-relay system” that works as molecular switches modulating the conformation. The principal element of the event points at interactions of charged residues that appear crucial for the transporter dynamics and function. Moreover, hOAT1 model was embedded in different lipid bilayer membranes highlighting the crucial structural dependence on lipid-protein interactions. MD simulations supported the pivotal role of phosphatidylethanolamine components to the protein conformation stability. The present model is made available to decipher the impact of any observed polymorphism and mutation on drug transport as well as to understand substrate binding modes

Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale

The Organic Anion Transporter 1 is a membrane transporter known for its central role in drug elimination by the kidney. hOAT1 is an antiporter translocating substrate in exchange for a-ketoglutarate. The understanding of hOAT1 structure and function remains limited due to the absence of resolved structure of hOAT1. Benefiting from conserved structural and functional patterns shared with other Major Facilitator Superfamily transporters, the present study intended to investigate fragments of hOAT1 transport function and modulation of its activity in order to make a step forward the understanding of its transport cycle. μs-long molecular dynamics simulation of hOAT1 were carried out suggesting two plausible binding sites for a typical substrate, adefovir, in line with experimental observations. The well-known B-like motif binding site was observed in line with previous studies. However, we here propose a new inner binding cavity which is expected to be involved in substrate translocation event. Binding modes of hOAT1 co-substrate α-ketoglutarate were also investigated suggesting that it may bind to highly conserved intracellular motifs. We here hypothesise that α-ketoglutarate may disrupt the pseudo-symmetrical intracellular charge-relay system which in turn may participate to the destabilisation of OF conformation. Investigations regarding allosteric communications along hOAT1 also suggest that substrate binding event might modulate the dynamics of intracellular charge relay system, assisted by surrounding lipids as active partners. We here proposed a structural rationalisation of transport impairments observed for two single nucleotide polymorphisms, p.Arg50His and p.Arg454Gln suggesting that the present model may be used to transport dysfunctions arising from hOAT1 mutations

Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3)LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest.FDM acknowledges financial support from the Swedish Research Council (Grant No. 621-2014-4646) and SNIC (Swedish National Infrastructure for Computing) for providing computer resources. The work in Limoges (IB and PT) is supported by the “Conseil Régional du Limousin”. PT gratefully acknowledges the support by the Operational Program Research and Development Fund (project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic). IB gratefully acknowledges financial support from “Association Djerbienne en France”

Antioxidant-inspired drug discovery: antitumor metabolite is formed in situ from a hydroxycinnamic acid derivative upon free radical scavenging

Cancer cells generally possess higher levels of reactive oxygen species than normal cells, and this can serve as a possible therapeutic target. In this proof-of-concept study, an antioxidant-inspired drug discovery strategy was evaluated using a hydroxycinnamic acid derivative. The processing of oxidized mixtures of p-coumaric acid methyl ester (pcm) revealed a new antitumor lead, graviquinone. Graviquinone bypassed ABCB1-mediated resistance, induced DNA damage in lung carcinoma cells but exerted DNA protective activity in normal keratinocytes, and modulated DNA damage response in MCF-7 cells. The cytotoxic effect of pcm in MCF-7 cells was potentiated under H2O2-induced oxidative stress, and the formation of graviquinone was confirmed by Fenton's reaction on pcm. In silico density functional theory calculations suggested graviquinone as a kinetic product of pcm-scavenging (OH)-O-center dot radicals. Our results demonstrate the pharmacological value of an in situ-formed, oxidative stress-related metabolite of an antioxidant. This might be of particular importance for designing new strategies for antioxidant-based drug discovery

Consequences of conformational flexibility in hydrogen-bond-driven self-assembly processes

We report the synthesis and self-assembly of chiral, conformationally flexible C3-symmetrical trisamides. A strong Cotton effect is observed for the supramolecular polymers in linear alkanes but not in cyclic alkanes. MD simulations suggest 2:1 conformations of the amides within the aggregates in both types of solvents, but a chiral bias in only linear alkanes.JAB, MGI, RPAG, EWM and ARAP would like to thank the Gravity program 024.001.035, NWO TOP-PUNT 718.014.003 for financial support and Anneloes Oude Vrielink for TEM imaging. FDM and ML acknowledge the Swedish e-Research Center (SeRC) for financial support, the Swedish Research Council (Grant No. 621-2014-4646), SNIC (Swedish National Infrastructure for Computing) and Dr Julien Idé for providing the code for exciton coupling calculations