Effect of Substituents on the Photodynamic Action of Anthraquinones: EPR, Computational and In Vitro Studies

Anthraquinone class of compounds possesses a broad spectrum of therapeutic applications. Cancer cell targeting ability, together with photogeneration of reactive oxygen species, renders anthraquinones an interesting class of photosensitizers for photodynamic therapy (PDT). Screening of newer compounds for better singlet oxygen generation is of current interest to improve the practical usability in PDT. In this study, we investigate the photodynamic activity of nine commercially available anthraquinones, using EPR spectroscopy and computational techniques, to identify the role of substituents on singlet oxygen yield. Three anthraquinone derivatives, 1,5-diaminoanthraquinone, 15-dihydroxyanthraquinone and 1,2,7-trihydroxyanthraquinone, showed highest singlet oxygen quantum yield (0.21, 0.18 and 0.15, respectively) relative to Rose Bengal. Time-dependent density functional theory calculations indicate the singlet oxygen quantum yield of anthraquinones inversely correlate well with the excited singlet-triplet (S1-T1) energy gap. Electron-donating substituents present at positions 1, 2 and 5 of anthraquinone seem to reduce the S1-T1 energy gap, facilitating inter-system crossing and the production of singlet oxygen. This would greatly aid in the design of newer anthraquinone-based photosensitizers. This study also highlights the suitability of 1,5-diaminoanthraquinone for PDT applications as demonstrated by in vitro experiments of photoinduced DNA cleavage and photocytotoxicity in Dalton's lymphoma ascites.

Molecular Dynamics Studies on the Bacterial Membrane Pore Formation by Small Molecule Antimicrobial Agents

Antimicrobial peptides (AMPs) act on the membrane bilayer of pathogens, causing leakage in the membrane and cell death. Amphiphilic kaempferol derivatives possessing basic functional groups show excellent antibacterial activities, which has been proven through experimental techniques. These compounds are known to target negatively charged bacterial membranes. However, the detailed mechanism of action and their structure-activity relationship are not clear. In this work, we reported theoretical investigation on the mechanism of action of two previously reported kaempferol derivatives on a DMPC/DMPG mixed bilayer. Despite the rigid structure of the compounds when compared to AMPs, spontaneous pore formation in the membrane was not observed in 400 ns molecular dynamics (MD) simulations. MD simulations with biasing forces resulted in the formation of pores in the bilayer for the derivatives and not for kaempferol. The stability of the pores was assessed by pore closure timescales in unbiased MD simulations, which was found to be 5.3 and 17.0 ns for 2 and 3, respectively. Free energy change for the permeation into the bilayer for kaempferol (1), tertiary amine derivative (2), and arginine derivative (3) was calculated to be -1.5, -48.2, and -100.3 kJ/mol, respectively, which correlate with their antibacterial activity. Furthermore, our results indicate that compound 3 forms a stable toroidal pore in the membrane when multiple molecules are oriented in a transmembrane configuration. Our work sheds light on the mechanism of action of small molecule antimicrobial agents, which can be exploited for the rational design of drug candidates.

Computational modeling and experimental validation of the EPI-X4/CXCR4 complex allows rational design of small peptide antagonists

EPI-X4, a 16-mer fragment of albumin, is a specific endogenous antagonist and inverse agonist of the CXC-motif-chemokine receptor 4 (CXCR4) and thus a key regulator of CXCR4 function. Accordingly, activity-optimized synthetic derivatives of EPI-X4 are promising leads for the therapy of CXCR4-linked disorders such as cancer or inflammatory diseases. We investigated the binding of EPI-X4 to CXCR4, which so far remained unclear, by means of biomolecular simulations combined with experimental mutagenesis and activity studies. We found that EPI-X4 interacts through its N-terminal residues with CXCR4 and identified its key interaction motifs, explaining receptor antagonization. Using this model, we developed shortened EPI-X4 derivatives (7-mers) with optimized receptor antagonizing properties as new leads for the development of CXCR4 inhibitors. Our work reveals the molecular details and mechanism by which the first endogenous peptide antagonist of CXCR4 interacts with its receptor and provides a foundation for the rational design of improved EPI-X4 derivatives.

An optimized derivative of an endogenous CXCR4 antagonist prevents atopic dermatitis and airway inflammation

Aberrant CXCR4/CXCL12 signaling is involved in many pathophysiological processes such as cancer and inflammatory diseases. A natural fragment of serum albumin, named EPI-X4, has previously been identified as endogenous peptide antagonist and inverse agonist of CXCR4 and is a promising compound for the development of improved analogues for the therapy of CXCR4-associated diseases. To generate optimized EPI-X4 derivatives we here performed molecular docking analysis to identify key interaction motifs of EPI-X4/CXCR4. Subsequent rational drug design allowed to increase the anti-CXCR4 activity of EPI-X4. The EPI-X4 derivative JM#21 bound CXCR4 and suppressed CXCR4-tropic HIV-1 infection more efficiently than the clinically approved small molecule CXCR4 antagonist AMD3100. EPI-X4 JM#21 did not exert toxic effects in zebrafish embryos and suppressed allergen-induced infiltration of eosinophils and other immune cells into the airways of animals in an asthma mouse model. Moreover, topical administration of the optimized EPI-X4 derivative efficiently prevented inflammation of the skin in a mouse model of atopic dermatitis. Thus, rationally designed EPI-X4 JM#21 is a novel potent antagonist of CXCR4 and the first CXCR4 inhibitor with therapeutic efficacy in atopic dermatitis. Further clinical development of this new class of CXCR4 antagonists for the therapy of atopic dermatitis, asthma and other CXCR4-associated diseases is highly warranted.

How Protic Solvents Determine the Reaction Mechanisms of Diphenylcarbene in Solution

We investigate the effects of small admixtures of protic solvent molecules, such as water and alcohols, on the ultrafast dynamics of diphenylcarbene in acetonitrile at room temperature. Broadband transient absorption measurements and quantum mechanics/molecular mechanics molecular dynamics simulations allow elucidating the dominant reaction mechanism of an intermediate hydrogen-bonded complex between singlet diphenylcarbene and a protic solvent molecule, thus competing with intersystem crossing. Analysis of the data indicates that complex formation is a diffusion-controlled process with orientational requirements. The reaction path involving a benzhydryl cation is less likely in neat bulkier alcohols, as it requires the interaction of the carbene with a protic solvent molecule being part of a hydrogen-bonded network. The simulations indicate a further reaction path toward O-H insertion and two side reactions depending on the involved protic solvent species. Thus, we established that not only the number but also the chemical nature of the protic solvent molecule determine which reaction path is pursued.

Molecular recognition of carboxylates in the protein leucine zipper by a multivalent supramolecular ligand: residue-specific, sensitive and label-free probing by UV resonance Raman spectroscopy

Proof of concept study for using UVRR spectroscopy to monitor the selective binding of an artificial ligand to carboxylate residues of a protein.

A Multiperspective Approach to Solvent Regulation of Enzymatic Activity: HMG-CoA Reductase

3-Hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase was investigated in different organic cosolvents by means of kinetic and calorimetric measurements, molecular dynamics simulations, and small-angle X-ray scattering. The combined experimental and theoretical techniques were essential to complement each other's limitations in the investigation of the complex interaction pattern between the enzyme, different solvent types, and concentrations. In this way, the underlying mechanisms for the loss of enzyme activity in different water-miscible solvents could be elucidated. These include direct inhibitory effects onto the active center and structural distortions.

Competitive solvent-molecule interactions govern primary processes of diphenylcarbene in solvent mixtures

Photochemical reactions in solution often proceed via competing reaction pathways comprising intermediates that capture a solvent molecule. A disclosure of the underlying reaction mechanisms is challenging due to the rapid nature of these processes and the intricate identification of how many solvent molecules are involved. Here combining broadband femtosecond transient absorption and quantum mechanics/molecular mechanics simulations, we show for one of the most reactive species, diphenylcarbene, that the decision-maker is not the nearest solvent molecule but its neighbour. The hydrogen bonding dynamics determine which reaction channels are accessible in binary solvent mixtures at room temperature. In-depth analysis of the amount of nascent intermediates corroborates the importance of a hydrogen-bonded complex with a protic solvent molecule, in striking analogy to complexes found at cryogenic temperatures. Our results show that adjacent solvent molecules take the role of key abettors rather than bystanders for the fate of the reactive intermediate.

Photochemistry in solution often involves coexisting reaction channels that may comprise intermediates capturing a solvent molecule. Here, the authors show for one of the most reactive species, diphenylcarbene, that the decision-maker is not the nearest solvent molecule but its neighbour.

Switching the Spin State of Diphenylcarbene via Halogen Bonding

The interactions between diphenylcarbene DPC and the halogen bond donors CF3I and CF3Br were investigated using matrix isolation spectroscopy (IR, UV-vis, and EPR) in combination with QM and QM/MM calculations. Both halogen bond donors CF3X form very strong complexes with the singlet state of DPC, but only weakly interact with triplet DPC. This results in a switching of the spin state of DPC, the singlet complexes becoming more stable than the triplet complexes. CF3I forms a second complex (type II) with DPC that is thermodynamically slightly more stable. Calculations predict that in this second complex the DPC···I distance is shorter than the F3C···I distance, whereas in the first (type I) complex the DPC···I distance is, as expected, longer. CF3Br only forms the type I complex. Upon irradiation I or Br, respectively, are transferred to the DPC carbene center and radical pairs are formed. Finally, on annealing, the formal C-X insertion product of DPC is observed. Thus, halogen bonding is a powerful new principle to control the spin state of reactive carbenes.