A quantum crystallographic approach to short hydrogen bonds

Rapid eradication of vancomycin and methicillin-resistant Staphylococcus aureus by MDP1 antimicrobial peptide coated on photocrosslinkable chitosan hydrogel: in vitro antibacterial and in silico molecular docking studies

Introduction

Antibiotic resistance and weak bioavailability of antibiotics in the skin due to systemic administration leads to failure in eradication of vancomycin- and methicillin-resistant Staphylococcus aureus (VRSA and MRSA)-associated wound infections and subsequent septicemia and even death. Accordingly, this study aimed at designing a photocrosslinkable methacrylated chitosan (MECs) hydrogel coated by melittin-derived peptide 1 (MDP1) that integrated the antibacterial activity with the promising skin regenerative capacity of the hydrogel to eradicate bacteria by burst release strategy.

Methods

The MECs was coated with MDP1 (MECs-MDP1), characterized, and the hydrogel-peptide interaction was evaluated by molecular docking. Antibacterial activities of MECs-MDP1 were evaluated against VRSA and MRSA bacteria and compared to MECs-vancomycin (MECs-vanco). Antibiofilm activity of MECs-MDP1 was studied by our novel 'in situ biofilm inhibition zone (IBIZ)' assay, and SEM. Biocompatibility with human dermal fibroblast cells (HDFs) was also evaluated.

Results and Discussion

Molecular docking showed hydrogen bonds as the most interactions between MDP1 and MECs at a reasonable affinity. MECs-MDP1 eradicated the bacteria rapidly by burst release strategy whereas MECs-vanco failed to eradicate them at the same time intervals. Antibiofilm activity of MECs-MDP1 were also proved successfully. As a novel report, molecular docking analysis has demonstrated that MDP1 covers the structure of MECs and also binds to lysozyme with a reasonable affinity, which may explain the inhibition of lysozyme. MECs-MDP1 was also biocompatible with human dermal fibroblast skin cells, which indicates its safe future application. The antibacterial properties of a photocrosslinkable methacrylated chitosan-based hydrogel coated with MDP1 antimicrobial peptide were successfully proved against the most challenging antibiotic-resistant bacteria causing nosocomial wound infections; VRSA and MRSA. Molecular docking analysis revealed that MDP1 interacts with MECs mainly through hydrogen bonds with reasonable binding affinity. MECs-MDP1 hydrogels eradicated the planktonic state of bacteria by burst release of MDP1 in just a few hours whereas MECs-vanco failed to eradicate them. inhibition zone assay showed the anti-biofilm activity of the MECs-MDP1 hydrogel too. These findings emphasize that MECs-MDP1 hydrogel would be suggested as a biocompatible wound-dressing candidate with considerable and rapid antibacterial activities to prevent/eradicate VRSA/MRSA bacterial wound infections.

Influence of N-protonation on electronic properties of acridine derivatives by quantum crystallography

Applications of 9-aminoacridine (9aa) and its derivatives span fields such as chemistry, biology, and medicine, including anticancer and antimicrobial activities. Protonation of such molecules can alter their bioavailability as weakly basic drugs like aminoacridines exhibit reduced solubility at high pH levels potentially limiting their effectiveness in patients with elevated gastric pH. In this study, we analyse the influence of protonation on the electronic characteristics of the molecular organic crystals of 9-aminoacridine. The application of quantum crystallography, including aspherical atom refinement, has enriched the depiction of electron density in the studied systems and non-covalent interactions, providing more details than previous studies. Our experimental results, combined with a topological analysis of the electron density and its Laplacian, provided detailed descriptions of how protonation changes the electron density distribution around the amine group and water molecule, concurrently decreasing the electron density at bond critical points of N/O-H bonds. Protonation also alters the molecular architecture of the systems under investigation. This is reflected in different proportions of the N⋯H and O⋯H intermolecular contacts for the neutral and protonated forms. Periodic DFT calculations of the cohesive energies of the crystal lattice, as well as computed interaction energies between molecules in the crystal, confirm that protonation stabilises the crystal structure due to a positive synergy between strong halogen and hydrogen bonds. Our findings highlight the potential of quantum crystallography in predicting crystal structure properties and point to its possible applications in developing new formulations for poorly soluble drugs.

Variation in pnictogen-oxygen bonding unlocks greatly enhanced Brønsted basicity for the monomeric stibine oxide

Phosphine oxides and arsine oxides feature highly polarized pnictoryl groups (Pn+-O-/Pn = O; Pn = P, As) and react as Brønsted bases through O-centered lone pairs. We recently reported the first example of a monomeric stibine oxide, Dipp3SbO (Dipp = diisopropylphenyl), allowing periodic trends in pnictoryl bonding to be extended to antimony for the first time. Computational studies suggest that, as the pnictogen atom becomes heavier, delocalization of electron density from the O-centered lone pairs to the Pn-C σ* orbitals is attenuated, destabilizing the lone pairs and increasing the donor capacity of the pnictine oxide. Herein, we assess the Brønsted basicity of a series of monomeric pnictine oxides (Dipp3PnO; Pn = P, As, and Sb). Stoichiometric reactivity between Dipp3PnO and a series of acids demonstrates the greatly enhanced ability of Dipp3SbO to accept protons relative to the lighter congeners, consistent with theoretical isodesmic reaction enthalpies and proton affinities. 1H NMR spectrometric titrations allow for the pKaH,MeCN determination of Dipp3AsO and Dipp3SbO, revealing a 106-fold increase in Brønsted basicity from Dipp3AsO to Dipp3SbO. The increased basicity can be exploited in catalysis; Dipp3SbO exhibits dramatically increased catalytic efficiency in the Brønsted base-catalyzed transesterification between p-nitrophenyl acetate and 2,2,2-trifluoroethanol. Our results unambiguously confirm the drastic increase in Brønsted basicity from Dipp3PO < Dipp3AsO < Dipp3SbO, a direct consequence of the variation in the electronic structure of the pnictoryl bond as the pnictogen atom increases in atomic number.

Uncovering the role of non-covalent interactions in solid-state photoswitches by non-spherical structure refinements with NoSpherA2

We present a charge density study of two linkage isomer photoswitches, [Pd(Bu4dien)(NO2)]BPh4·THF (1) and [Ni(Et4dien)(NO2)2] (2) using Hirshfeld Atom Refinement (HAR) methods implemented via the NoSpherA2 interface in Olex2. HAR is used to explore the electron density distribution in the photoswitchable molecules of 1 and 2, to gain an in-depth understanding of key bonding features and their influence on the single-crystal-to-single-crystal reaction. HAR analysis is also combined with ab initio calculations to explore the non-covalent interactions that influence physical properties of the photoswitches, such as the stability of the excited state nitrito-(η1-ONO) isomer. This insight can be fed back into the crystal engineering process to develop new and improved photoswitches that can be optimised towards specific applications.

Importance of Nuclear Quantum Effects for Molecular Cocrystals with Short Hydrogen Bonds

Many efforts have been recently devoted to the design and investigation of multicomponent pharmaceutical solids, such as salts and cocrystals. The experimental distinction between these solid forms is often challenging. Here, we show that the transformation of a salt into a cocrystal with a short hydrogen bond does not occur as a sharp phase transition but rather a smooth shift of the positional probability of the hydrogen atoms. A combination of solid-state NMR spectroscopy, X-ray diffraction, and diffuse reflectance measurements with density functional theory calculations that include nuclear quantum effects (NQEs) provides evidence of temperature-induced hydrogen atom shift in cocrystals with short hydrogen bonds. We demonstrate that for the predictions of the salt/cocrystal solid forms with short H-bonds, the computations have to include NQEs (particularly hydrogen nuclei delocalization) and temperature effects.

X-ray wavefunction refinement and comprehensive structural studies on bromo-substituted analogues of 2-deoxy-d-glucose in solid state and solution

The structural studies on two bromo-substituted derivatives of 2-deoxy-d-glucose (2-DG), namely 2-deoxy-2-bromo-d-glucose (2-BG) and 2-deoxy-2-bromo-d-mannose (2-BM) are described. 2-DG itself is an inhibitor of hexokinase, the first enzyme in the glycolysis process, playing a vital role in both cancer cell metabolism and viral replication in host cells. Because of that, 2-DG derivatives are considered as potential anti-cancer and anti-viral drugs. An X-ray quantum crystallography approach allowed us to obtain more accurate positions of hydrogen atoms by applying Hirshfeld atom refinement, providing a better description of hydrogen bonding even in the case of data from routine X-ray experiments. Obtained structures showed that the introduction of bromine at the C2 position in the pyranose ring has a minor influence on its conformation but still, it has a noticeable effect on the crystal structure. Bromine imposes the formation of a layered supramolecular landscape containing hydrogen bonds, which involves the bromine atom. Periodic DFT calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings and highlighted energetic changes upon bromine substitution. Based on molecular wavefunction from the refinement, we calculated the electrostatic potential, Laplacian, and ELI-D, and applied them to charge-density studies, which confirmed the geometry of hydrogen bonding and involvement of the bromine atom with these intermolecular interactions. NMR studies in the solution show that both compounds do not display significant differences in their anomeric equilibria compared to 2-DG, and the pyranose ring puckering is similar in both aqueous and solid state.